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view LINKYX_mpileup_wrapper.sh @ 2:0d8315be76b7

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author biomonika
date Tue, 17 Feb 2015 21:59:51 -0500
parents 05c27700e5ca
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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