Mercurial > repos > ulfschaefer > phe_samtools_mpileup
view phe_samtools_mpileup.sh @ 14:9a474dd2ba4d draft
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author | ulfschaefer |
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date | Thu, 30 Jun 2016 03:56:40 -0400 |
parents | f78ed0f61f52 |
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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