Mercurial > repos > biomonika > monika_mpileup
changeset 16:0b2d6cee9f2e draft
Uploaded
| author | biomonika |
|---|---|
| date | Wed, 13 Aug 2014 16:51:25 -0400 |
| parents | 7f57b3213b2b |
| children | 46044d94ee63 |
| files | LINKYX_mpileup_wrapper.sh |
| diffstat | 1 files changed, 7 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LINKYX_mpileup_wrapper.sh Wed Aug 13 16:51:25 2014 -0400 @@ -0,0 +1,7 @@ +#!/bin/bash +results=$1; +bam_file=$2; +reference=$3; + +#samtools mpileup -uf $reference $2 >$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