Mercurial > repos > ulfschaefer > phe_samtools_mpileup

comparison phe_samtools_mpileup.sh @ 0:3dd238a07d9b draft default tip

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author ulfschaefer
date Tue, 19 Apr 2016 07:33:10 -0400
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1 #!/bin/bash
2
3 echo $@
4
5 BAM=$1
6 shift
7 REF=$1
8 shift
9 OUTVCF=$1
10
11 CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $BAM | bcftools call -m -f GQ > $OUTVCF"
12
13 echo "CMD: "$CMD
14 eval $CMD