diff --git a/GATK_00_PrepareRef.sh b/GATK_00_PrepareRef.sh index 37142cf..20c9007 100755 --- a/GATK_00_PrepareRef.sh +++ b/GATK_00_PrepareRef.sh @@ -18,7 +18,7 @@ samtools faidx ${REF} bwa index -a bwtsw ${REF} FIL # Create interval list (here 100 kb intervals) -python fasta_length.py ${REF} > ${REF%.*}_length.txt +fasta_length.py ${REF} > ${REF%.*}_length.txt bedtools makewindows -w 100000 -g ${REF%.*}_length.txt > ${REF%.*}_100kb_coords.bed java -Xmx100G -jar $PICARD_HOME/picard.jar BedToIntervalList \ INPUT=${REF%.*}_100kb_coords.bed \