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view LINKYX_mpileup_wrapper.sh @ 5:939e59027486

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edited README
author biomonika <biomonika@psu.edu>
date Fri, 20 Feb 2015 14:55:29 -0500
parents 0d8315be76b7
children
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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