diff --git a/workflow/scripts/locus_coverage.sh b/workflow/scripts/locus_coverage.sh index a0b396c3c..d4d49d375 100755 --- a/workflow/scripts/locus_coverage.sh +++ b/workflow/scripts/locus_coverage.sh @@ -22,10 +22,7 @@ for dir in $DIRS; do bam=`ls $dir/*.bam`; sample=`basename $bam | sed 's/\.bam//g'`; - #cov=`samtools view -b -q 30 $bam | bedtools coverage -a ${REF_BED} -b stdin | cut -f 8 | tr '\n' '\t'`; cov=`samtools view -b -q 30 $bam | bedtools coverage -a ${REF_BED} -b stdin | cut -f 8 | tr '\n' '\t'`; dep=`samtools view -b -q 30 $bam | bedtools coverage -a ${REF_BED} -b stdin -mean | cut -f 5 | tr '\n' '\t'`; - #echo -e "$sample\t$cov"; echo -e "$sample\t${cov}\t${dep}"; - exit done