# HG changeset patch
# User ulfschaefer
# Date 1450700689 18000
# Node ID 65b5406977c98f634e8b49793b39852130c4a166
# Parent  7ec666e2f315d3b69d960931ab321666f31945cd
Uploaded

diff -r 7ec666e2f315 -r 65b5406977c9 phe_samtools_mpileup.sh
--- /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