Mercurial > repos > biomonika > linkyx

view LINKYX_mpileup_wrapper.sh @ 25:ffe50d004cb4

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samtools sort, echo path
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 22:01:22 -0400
parents 7997c93ee479
children
line wrap: on
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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