Mercurial > repos > ulfschaefer > phe_samtools_mpileup
changeset 3:65b5406977c9 draft
Uploaded
author | ulfschaefer |
---|---|
date | Mon, 21 Dec 2015 07:24:49 -0500 |
parents | 7ec666e2f315 |
children | 5b63d9a21d01 |
files | phe_samtools_mpileup.sh |
diffstat | 1 files changed, 21 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phe_samtools_mpileup.sh Mon Dec 21 07:24:49 2015 -0500 @@ -0,0 +1,21 @@ +#!/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