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view LINKYX_mpileup_wrapper.sh @ 32:cf7cd22fc5d3 default tip

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author biomonika
date Tue, 10 Feb 2015 12:09:34 -0500
parents 7997c93ee479
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#!/bin/bash
results=$1;
bam_file=$2;
reference=$3;

sorted_bam=${bam_file}_sorted

samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results