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Pool_configuration.cfg
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Pool_configuration.cfg
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[INPUT]
sample_names: NGS01672-NextSeq500-ExomeVCRome-Roche-P5-Run150813-DIS320_S3_align.realign.recal.bam,NGS01671-NextSeq500-ExomeVCRome-Roche-P5-Run150813-DIS319_S2_align.realign.recal.bam,NGS01670-NextSeq500-ExomeVCRome-Roche-P5-Run150813-DIS118_S1_align.realign.recal.bam
alignment_path : /ingemm/scratch/Exomas/Trios_KH/Trio4/v3/LACONv/bam_files
analysis_bed : /ingemm/ref/Bed_referencia/Exoma/exoma_v2_s20.bed
sample_gender : H,M,H
[OUTPUT]
alignment_path : /ingemm/scratch/Exomas/Trios_KH/Trio4/v3/LACONv/bam_files
cnv_path: /ingemm/scratch/Exomas/Trios_KH/Trio4/v3/LACONv/CNV
coverage_path: /ingemm/scratch/Exomas/Trios_KH/Trio4/v3/LACONv/coverage
[REFERENCE]
ref_fasta : /ingemm/ref/Ref/hg19/fasta/ucsc.hg19.fasta
ref_fasta_cnv : /ingemm/ref/Ref/hg19/fasta/chr1toY.fasta
ref_fasta_cnv_index : /ingemm/ref/Ref/hg19/fasta/chr1toY.fasta.fai
control_cnv : /ingemm/ref/DBs/Data/
[BDs]
annotation_bed : /ingemm/ref/DBs/Data/annotation_refseq.bed
annotation_file : /ingemm/ref/DBs/Data/annotation_refseq.tsv
[SOFTWARE]
gatk_path : /opt/gatk/GenomeAnalysisTK.jar