Mercurial > repos > ulfschaefer > phe_samtools_mpileup
view phe_samtools_mpileup.sh @ 6:ae6b5f55733c draft
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author | ulfschaefer |
---|---|
date | Mon, 21 Dec 2015 08:50:11 -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