Mercurial > repos > ulfschaefer > phe_samtools_mpileup

changeset 3:65b5406977c9 draft

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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(-) [+]
line wrap: on
line diff
--- /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