Mercurial > repos > ulfschaefer > phe_samtools_mpileup

diff phe_samtools_mpileup.sh @ 0:c91df5df0faf draft

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author ulfschaefer
date Mon, 21 Dec 2015 07:12:34 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe_samtools_mpileup.sh	Mon Dec 21 07:12:34 2015 -0500
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+echo $@
+
+SAM=$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 $TMPBAM2.bam | bcftools call -m -f GQ > $OUTVCF"
+
+echo "CMD: "$CMD
+eval $CMD
+rm $TMPBAM
+rm $TMPBAM2.bam