Mercurial > repos > biomonika > linkyx
diff LINKYX_mpileup_wrapper.sh @ 0:05c27700e5ca
initial commit
| author | biomonika <biomonika@psu.edu> |
|---|---|
| date | Thu, 04 Sep 2014 18:24:19 -0400 |
| parents | |
| children | 0d8315be76b7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LINKYX_mpileup_wrapper.sh Thu Sep 04 18:24:19 2014 -0400 @@ -0,0 +1,12 @@ +#!/bin/bash +results=$1; +bam_file=$2; +reference=$3; + +sorted_bam=${bam_file}_sorted + +#LINKYX_PATH set during toolshed installation + +samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results + +#samtools mpileup -uf $reference $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt \ No newline at end of file