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view phe_samtools_mpileup.sh @ 0:c91df5df0faf draft

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author ulfschaefer
date Mon, 21 Dec 2015 07:12:34 -0500
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#!/bin/bash

echo $@

SAM=$1
shift
REF=$1
shift
OUTVCF=$1

TMPBAM=$$.tmpbam
TMPBAM2=$$.tmpbam2

samtools view -bS $SAM > $TMPBAM
samtools sort $TMPBAM $TMPBAM2

CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $TMPBAM2.bam | bcftools call -m -f GQ > $OUTVCF"

echo "CMD: "$CMD
eval $CMD
rm $TMPBAM
rm $TMPBAM2.bam