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view phe_samtools_mpileup.sh @ 10:f78ed0f61f52 draft

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author ulfschaefer
date Mon, 21 Dec 2015 10:17:45 -0500
parents 65b5406977c9
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#!/bin/bash

echo $@

BAM=$1
shift
REF=$1
shift
OUTVCF=$1

CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $BAM | bcftools call -m -f GQ > $OUTVCF"

echo "CMD: "$CMD
eval $CMD