Mercurial > repos > biomonika > linkyx

view LINKYX_mpileup_wrapper.sh @ 14:b5b14e3e3c61

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toolshed13
author biomonika <biomonika@psu.edu>
date Wed, 10 Sep 2014 11:07:54 -0400
parents 1955f03f092e
children ea52ef8d7f3a
line wrap: on
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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