families_map.sh

bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_F.fastq.gz | samtools sort -o families/30.004/map/30.004_F.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_M.fastq.gz | samtools sort -o families/30.004/map/30.004_M.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_1.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_2.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_3.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_4.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_5.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_6.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_7.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_8.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_9.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_10.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_11.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_12.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_13.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_14.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_15.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_16.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_17.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_18.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_19.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_20.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_21.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_22.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_23.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_24.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_25.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_26.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_27.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_28.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_29.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_30.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_31.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_32.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_33.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_34.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_35.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_36.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_37.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_38.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_39.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_40.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_41.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_42.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_43.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_44.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_45.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_46.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_47.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_48.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_49.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_50.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_51.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_52.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_53.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_54.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_55.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_56.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_57.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_58.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_59.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_60.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_61.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_62.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_63.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_64.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_65.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_66.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_67.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_68.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_69.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_70.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_71.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_72.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_73.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_74.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_75.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_76.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_77.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_78.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_79.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_80.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_81.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_82.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_83.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_84.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_85.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_86.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_87.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_88.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_89.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_90.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_91.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_92.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_93.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_94.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_95.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_96.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_96.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_97.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_97.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_98.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_98.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_99.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_99.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_100.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_100.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_101.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_101.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_102.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_102.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_103.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_103.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_104.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_104.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_105.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_105.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_106.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_106.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_107.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_107.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_108.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_108.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_109.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_109.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_110.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_110.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_111.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_111.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_112.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_112.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_113.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_113.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_114.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_114.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_115.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_115.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_116.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_116.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_117.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_117.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_118.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_118.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_119.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_119.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_120.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_120.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_121.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_121.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_122.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_122.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_123.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_123.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_124.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_124.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_125.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_125.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_126.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_126.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_127.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_127.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_128.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_128.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_129.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_129.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_130.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_130.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_131.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_131.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_132.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_132.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_133.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_133.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_134.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_134.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_135.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_135.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_136.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_136.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_137.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_137.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_138.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_138.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_139.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_139.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_140.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_140.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_141.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_141.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_142.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_142.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_143.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_143.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_144.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_144.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_145.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_145.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_146.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_146.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_147.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_147.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_148.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_148.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_149.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_149.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_150.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_150.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_151.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_151.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_152.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_152.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_153.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_153.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_154.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_154.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_155.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_155.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_156.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_156.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_157.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_157.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_158.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_158.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_159.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_159.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_160.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_160.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_161.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_161.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_162.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_162.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_163.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_163.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_164.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_164.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_165.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_165.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_pre_166.fastq.gz | samtools sort -o families/30.004/map/30.004_pre_166.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_1.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_2.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_3.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_4.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_5.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_6.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_7.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_8.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_9.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_10.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_11.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_12.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_13.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_14.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_15.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_16.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_17.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_18.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_19.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_20.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_21.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_22.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_23.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_24.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_25.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_26.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_27.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_28.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_29.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_30.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_31.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_32.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_33.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_34.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_35.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_36.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_37.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_38.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_39.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_40.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_41.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_42.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_43.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_44.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_45.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_46.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_47.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_48.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_49.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_50.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_51.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_52.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_53.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_54.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_55.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_56.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_57.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_58.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_59.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_60.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_61.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_62.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_63.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_64.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_65.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_66.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_67.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_68.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_69.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_70.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_71.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_72.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_73.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_74.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_75.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_76.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_77.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_78.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_79.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_80.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_81.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_82.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_83.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_84.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_85.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_86.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_87.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_88.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_89.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_90.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_91.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_92.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_93.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_94.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep1_95.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep1_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_1.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_2.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_3.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_4.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_5.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_6.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_7.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_8.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_9.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_10.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_11.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_12.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_13.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_14.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_15.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_16.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_17.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_18.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_19.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_20.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_21.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_22.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_23.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_24.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_25.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_26.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_27.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_28.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_29.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_30.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_31.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_32.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_33.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_34.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_35.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_36.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_37.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_38.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_39.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_40.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_41.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_42.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_43.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_44.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_45.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_46.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_47.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_48.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_49.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_50.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_51.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_52.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_53.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_54.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_55.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_56.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_57.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_58.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_59.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_60.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_61.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_62.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_63.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_64.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_65.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_66.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_67.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_68.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_69.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_70.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_71.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_72.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_73.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_74.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_75.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_76.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_77.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_78.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_79.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_80.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_81.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_82.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_83.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_84.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_85.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_86.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_87.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_88.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_89.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_90.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_91.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_92.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_93.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_94.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_95.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_96.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_96.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_97.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_97.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_98.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_98.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_99.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_99.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_100.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_100.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_101.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_101.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_102.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_102.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_103.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_103.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_104.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_104.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_105.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_105.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_106.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_106.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_107.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_107.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_108.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_108.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_109.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_109.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_110.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_110.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_111.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_111.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_112.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_112.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_113.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_113.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_114.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_114.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_115.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_115.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_116.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_116.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_117.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_117.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_118.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_118.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_119.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_119.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_120.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_120.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_121.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_121.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_122.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_122.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_123.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_123.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_124.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_124.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_125.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_125.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_126.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_126.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_127.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_127.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_128.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_128.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_129.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_129.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_130.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_130.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_131.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_131.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_132.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_132.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep2_133.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep2_133.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_1.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_2.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_3.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_4.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_5.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_6.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_7.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_8.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_9.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_10.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_11.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_12.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_13.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_14.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_15.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_16.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_17.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_18.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_19.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_20.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_21.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_22.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_23.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_24.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_25.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_26.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_27.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_28.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_29.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_30.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_31.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_32.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_33.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_34.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_35.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_36.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_37.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_38.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_39.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_40.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_41.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_42.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_43.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_44.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_45.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_46.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_47.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_48.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_49.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_50.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_51.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_52.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_53.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_54.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_55.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_56.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_57.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_58.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_59.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_60.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_61.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_62.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_63.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_64.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_65.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_66.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_67.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_68.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_69.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_70.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_71.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_72.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_73.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_74.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_75.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_76.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_77.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_78.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_79.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_80.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_81.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_82.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_83.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_84.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_85.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_86.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_87.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_88.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_89.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_90.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_91.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_92.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_93.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_94.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_95.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_96.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_96.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_97.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_97.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_98.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_98.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_99.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_99.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_100.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_100.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_101.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_101.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_102.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_102.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_103.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_103.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_104.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_104.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_105.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_105.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_106.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_106.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_107.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_107.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_108.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_108.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_109.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_109.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_110.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_110.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_111.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_111.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_112.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_112.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_113.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_113.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_114.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_114.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_115.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_115.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_116.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_116.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_117.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_117.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_118.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_118.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_119.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_119.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_120.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_120.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_121.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_121.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_122.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_122.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_123.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_123.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.004/trim/30.004_post_rep3_124.fastq.gz | samtools sort -o families/30.004/map/30.004_post_rep3_124.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_F.fastq.gz | samtools sort -o families/30.058/map/30.058_F.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_M.fastq.gz | samtools sort -o families/30.058/map/30.058_M.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_1.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_2.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_3.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_4.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_5.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_6.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_7.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_8.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_9.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_10.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_11.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_12.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_13.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_14.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_15.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_16.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_17.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_18.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_19.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_20.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_21.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_22.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_23.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_24.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_25.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_26.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_27.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_28.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_29.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_30.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_31.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_32.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_33.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_34.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_35.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_36.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_37.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_38.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_39.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_40.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_41.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_42.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_43.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_44.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_45.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_46.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_47.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_48.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_49.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_50.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_51.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_52.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_53.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_54.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_55.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_56.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_57.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_58.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_59.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_60.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_61.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_62.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_63.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_64.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_65.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_66.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_67.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_68.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_69.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_70.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_71.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_72.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_73.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_74.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_75.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_76.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_77.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_78.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_79.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_80.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_81.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_82.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_83.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_84.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_85.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_86.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_87.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_88.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_89.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_90.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_91.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_92.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_93.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_94.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_95.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_96.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_96.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_97.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_97.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_98.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_98.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_99.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_99.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_100.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_100.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_101.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_101.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_102.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_102.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_103.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_103.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_104.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_104.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_105.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_105.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_106.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_106.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_107.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_107.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_108.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_108.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_109.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_109.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_110.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_110.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_111.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_111.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_112.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_112.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_113.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_113.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_114.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_114.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_115.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_115.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_116.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_116.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_117.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_117.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_118.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_118.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_119.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_119.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_120.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_120.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_121.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_121.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_122.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_122.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_123.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_123.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_124.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_124.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_125.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_125.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_126.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_126.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_127.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_127.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_128.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_128.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_129.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_129.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_130.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_130.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_131.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_131.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_132.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_132.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_133.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_133.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_134.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_134.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_135.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_135.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_136.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_136.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_137.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_137.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_138.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_138.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_139.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_139.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_140.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_140.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_141.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_141.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_142.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_142.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_143.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_143.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_144.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_144.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_145.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_145.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_146.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_146.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_147.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_147.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_148.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_148.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_149.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_149.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_150.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_150.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_151.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_151.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_152.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_152.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_153.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_153.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_154.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_154.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_155.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_155.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_156.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_156.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_157.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_157.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_158.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_158.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_159.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_159.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_160.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_160.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_161.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_161.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_162.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_162.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_163.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_163.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_164.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_164.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_165.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_165.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_166.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_166.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_167.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_167.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_168.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_168.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_169.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_169.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_170.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_170.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_171.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_171.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_172.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_172.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_173.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_173.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_pre_174.fastq.gz | samtools sort -o families/30.058/map/30.058_pre_174.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_1.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_2.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_3.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_4.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_5.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_6.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_7.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_8.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_9.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_10.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_11.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_12.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_13.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_14.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_15.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_16.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_17.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_18.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_19.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_20.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_21.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_22.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_23.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_24.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_25.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_26.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_27.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_28.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_29.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_30.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_31.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_32.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_33.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_34.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_35.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_36.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_37.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_38.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_39.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_40.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_41.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_42.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_43.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_44.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_45.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_46.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_47.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_48.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep1_49.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep1_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_1.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_2.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_3.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_4.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_5.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_6.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_7.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_8.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_9.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_10.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_11.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_12.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_13.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_14.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_15.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_16.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_17.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_18.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_19.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_20.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_21.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_22.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_23.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_24.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_25.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_26.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_27.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_28.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_29.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_30.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_31.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_32.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_33.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_34.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_35.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_36.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_37.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_38.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_39.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_40.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_41.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep2_42.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep2_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_1.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_2.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_3.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_4.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_5.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_6.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_7.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_8.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_9.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_10.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_11.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_12.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_13.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_14.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_15.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_16.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_17.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_18.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_19.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_20.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_21.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_22.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_23.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_24.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_25.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_26.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_27.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_28.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_29.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_30.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_31.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_32.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_33.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_34.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_35.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_36.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_37.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_38.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_39.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_40.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_41.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_42.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_43.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_44.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_45.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_46.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_47.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_48.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_49.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_50.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_51.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_52.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_53.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.058/trim/30.058_post_rep3_54.fastq.gz | samtools sort -o families/30.058/map/30.058_post_rep3_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_F.fastq.gz | samtools sort -o families/30.062/map/30.062_F.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_M.fastq.gz | samtools sort -o families/30.062/map/30.062_M.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_1.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_2.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_3.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_4.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_5.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_6.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_7.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_8.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_9.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_10.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_11.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_12.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_13.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_14.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_15.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_16.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_17.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_18.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_19.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_20.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_21.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_22.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_23.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_24.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_25.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_26.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_27.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_28.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_29.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_30.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_31.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_32.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_33.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_34.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_35.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_36.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_37.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_38.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_39.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_40.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_41.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_42.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_43.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_44.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_45.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_46.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_47.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_48.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_49.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_50.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_51.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_52.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_53.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_54.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_55.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_56.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_57.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_58.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_59.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_60.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_61.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_62.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_63.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_64.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_65.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_66.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_67.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_68.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_69.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_70.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_71.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_72.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_73.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_74.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_75.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_76.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_77.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_78.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_79.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_80.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_81.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_82.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_83.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_84.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_85.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_86.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_87.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_88.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_89.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_90.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_91.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_92.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_93.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_94.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_95.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_96.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_96.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_97.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_97.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_98.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_98.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_99.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_99.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_100.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_100.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_101.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_101.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_102.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_102.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_103.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_103.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_104.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_104.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_105.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_105.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_106.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_106.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_107.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_107.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_108.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_108.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_109.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_109.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_110.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_110.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_111.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_111.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_112.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_112.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_113.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_113.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_114.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_114.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_115.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_115.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_116.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_116.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_117.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_117.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_118.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_118.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_119.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_119.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_120.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_120.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_121.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_121.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_122.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_122.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_123.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_123.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_124.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_124.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_125.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_125.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_126.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_126.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_127.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_127.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_128.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_128.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_129.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_129.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_130.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_130.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_131.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_131.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_132.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_132.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_133.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_133.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_134.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_134.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_135.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_135.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_136.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_136.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_137.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_137.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_138.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_138.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_139.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_139.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_140.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_140.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_141.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_141.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_pre_142.fastq.gz | samtools sort -o families/30.062/map/30.062_pre_142.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_1.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_2.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_3.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_4.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_5.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_6.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_7.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_8.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_9.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_10.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_11.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_12.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_13.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_14.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_15.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_16.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_17.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_18.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_19.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_20.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_21.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_22.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_23.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_24.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_25.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_26.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_27.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_28.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_29.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_30.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_31.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_32.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_33.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_34.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_35.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_36.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_37.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_38.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_39.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_40.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_41.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_42.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_43.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_44.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_45.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_46.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_47.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_48.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_49.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_50.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_51.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_52.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_53.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_54.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_55.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_56.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_57.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_58.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_59.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_60.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_61.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_62.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_63.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_64.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_65.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_66.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_67.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_68.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_69.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_70.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_71.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_72.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_73.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_74.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_75.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_76.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_77.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_78.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_79.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_80.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_81.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_82.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_83.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_84.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_85.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_86.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_87.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_88.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_89.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_90.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_91.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_92.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_93.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_94.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_95.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_96.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_96.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_97.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_97.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_98.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_98.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_99.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_99.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_100.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_100.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_101.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_101.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_102.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_102.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_103.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_103.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_104.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_104.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep1_105.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep1_105.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_1.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_2.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_3.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_4.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_5.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_6.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_7.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_8.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_9.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_10.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_11.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_12.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_13.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_14.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_15.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_16.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_17.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_18.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_19.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_20.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_21.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_22.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_23.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_24.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_25.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_26.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_27.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_28.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_29.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_30.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_31.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_32.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_33.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_34.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_35.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_36.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_37.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_38.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_39.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_40.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_41.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_42.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_43.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_44.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_45.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_46.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_47.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_48.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_49.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_50.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_51.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_52.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_53.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_54.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_55.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_56.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_57.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_58.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_59.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_60.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_61.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_62.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_63.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_64.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_65.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_66.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_67.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_68.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_69.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_70.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_71.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_72.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_73.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_74.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_75.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_76.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_77.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_78.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_79.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_80.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_81.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep2_82.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep2_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_1.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_2.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_3.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_4.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_5.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_6.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_7.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_8.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_9.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_10.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_11.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_12.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_13.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_14.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_15.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_16.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_17.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_18.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_19.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_20.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_21.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_22.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_23.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_24.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_25.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_26.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_27.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_28.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_29.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_30.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_31.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_32.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_33.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_34.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_35.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_36.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_37.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_38.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_39.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_40.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_41.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_42.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_43.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_44.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_45.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_46.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_47.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_48.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_49.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_50.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_51.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_52.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_53.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_54.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_55.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_56.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_57.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_58.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_59.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_60.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_61.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_62.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_63.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_64.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_65.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_66.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_67.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.062/trim/30.062_post_rep3_68.fastq.gz | samtools sort -o families/30.062/map/30.062_post_rep3_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_F.fastq.gz | samtools sort -o families/30.065/map/30.065_F.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_M.fastq.gz | samtools sort -o families/30.065/map/30.065_M.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_1.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_2.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_3.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_4.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_5.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_6.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_7.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_8.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_9.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_10.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_11.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_12.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_13.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_14.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_15.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_16.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_17.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_18.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_19.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_20.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_21.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_22.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_23.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_24.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_25.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_26.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_27.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_28.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_29.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_30.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_31.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_32.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_33.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_34.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_35.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_36.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_37.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_38.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_39.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_40.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_41.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_42.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_43.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_44.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_45.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_46.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_47.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_48.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_49.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_50.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_51.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_52.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_53.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_54.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_55.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_56.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_57.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_58.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_59.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_60.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_61.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_62.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_63.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_64.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_65.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_66.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_67.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_68.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_69.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_70.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_71.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_72.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_73.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_74.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_75.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_76.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_77.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_78.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_79.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_80.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_81.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_82.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_83.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_pre_84.fastq.gz | samtools sort -o families/30.065/map/30.065_pre_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_1.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_2.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_3.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_4.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_5.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_6.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_7.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_8.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_9.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_10.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_11.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_12.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_13.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_14.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_15.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_16.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_17.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_18.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_19.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_20.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_21.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_22.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_23.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_24.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_25.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_26.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_27.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_28.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_29.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_30.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_31.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_32.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_33.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_34.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_35.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_36.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_37.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_38.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_39.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_40.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_41.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_42.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_43.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_44.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_45.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_46.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_47.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_48.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_49.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_50.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_51.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_52.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_53.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_54.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_55.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_56.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_57.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_58.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_59.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_60.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_61.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_62.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_63.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_64.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_65.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_66.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_67.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_68.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_69.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_70.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_71.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_72.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_73.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_74.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_75.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_76.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_77.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_78.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_79.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_80.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_81.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_82.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_83.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_84.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_85.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_86.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_87.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_88.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_89.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_90.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_91.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_92.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_93.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_94.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_95.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_96.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_96.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_97.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_97.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_98.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_98.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_99.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_99.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_100.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_100.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_101.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_101.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_102.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_102.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_103.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_103.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_104.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_104.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_105.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_105.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep1_106.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep1_106.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_1.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_2.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_3.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_4.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_5.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_6.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_7.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_8.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_9.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_10.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_11.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_12.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_13.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_14.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_15.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_16.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_17.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_18.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_19.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_20.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_21.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_22.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_23.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_24.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_25.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_26.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_27.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_28.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_29.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_30.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_31.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_32.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_33.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_34.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_35.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_36.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_37.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_38.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_39.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_40.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_41.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_42.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_43.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_44.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_45.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_46.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_47.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_48.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_49.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_50.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_51.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_52.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_53.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_54.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_55.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_56.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_57.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_58.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_59.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_60.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_61.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_62.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_63.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_64.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_65.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_66.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_67.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_68.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_69.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_70.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_71.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_72.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_73.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_74.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_75.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_76.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_77.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_78.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_79.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_79.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_80.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_80.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_81.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_81.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_82.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_82.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_83.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_83.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_84.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_84.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_85.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_85.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_86.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_86.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_87.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_87.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_88.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_88.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_89.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_89.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_90.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_90.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_91.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_91.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_92.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_92.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_93.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_93.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_94.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_94.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_95.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_95.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep2_96.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep2_96.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_1.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_1.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_2.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_2.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_3.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_3.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_4.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_4.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_5.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_5.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_6.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_6.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_7.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_7.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_8.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_8.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_9.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_9.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_10.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_10.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_11.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_11.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_12.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_12.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_13.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_13.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_14.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_14.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_15.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_15.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_16.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_16.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_17.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_17.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_18.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_18.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_19.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_19.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_20.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_20.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_21.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_21.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_22.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_22.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_23.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_23.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_24.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_24.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_25.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_25.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_26.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_26.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_27.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_27.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_28.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_28.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_29.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_29.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_30.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_30.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_31.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_31.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_32.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_32.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_33.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_33.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_34.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_34.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_35.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_35.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_36.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_36.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_37.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_37.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_38.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_38.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_39.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_39.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_40.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_40.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_41.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_41.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_42.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_42.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_43.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_43.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_44.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_44.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_45.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_45.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_46.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_46.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_47.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_47.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_48.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_48.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_49.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_49.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_50.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_50.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_51.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_51.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_52.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_52.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_53.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_53.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_54.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_54.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_55.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_55.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_56.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_56.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_57.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_57.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_58.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_58.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_59.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_59.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_60.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_60.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_61.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_61.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_62.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_62.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_63.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_63.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_64.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_64.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_65.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_65.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_66.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_66.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_67.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_67.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_68.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_68.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_69.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_69.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_70.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_70.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_71.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_71.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_72.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_72.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_73.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_73.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_74.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_74.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_75.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_75.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_76.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_76.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_77.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_77.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_78.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_78.bam
bwa mem -M Cgigas_RefSeq.fasta families/30.065/trim/30.065_post_rep3_79.fastq.gz | samtools sort -o families/30.065/map/30.065_post_rep3_79.bam