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author ulfschaefer
date Mon, 21 Dec 2015 09:00:43 -0500
parents 65b5406977c9
children f78ed0f61f52
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#!/bin/bash

echo $@

BAM=$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 $BAM | bcftools call -m -f GQ > $OUTVCF"

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