Mercurial > repos > biomonika > linkyx

view LINKYX_mpileup_wrapper.sh @ 0:05c27700e5ca

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author biomonika <biomonika@psu.edu>
date Thu, 04 Sep 2014 18:24:19 -0400
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children 0d8315be76b7
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#!/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