Mercurial > repos > ulfschaefer > phe_samtools_mpileup

diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe_samtools_mpileup.sh	Tue Apr 19 07:33:10 2016 -0400
@@ -0,0 +1,14 @@
+#!/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