# HG changeset patch
# User ulfschaefer
# Date 1450711065 18000
# Node ID f78ed0f61f52e756e2833c12a8456a0059f2fdfa
# Parent  17996fd454c642aa4f71b0586a42657d58eca0b9
Uploaded

diff -r 17996fd454c6 -r f78ed0f61f52 phe_samtools_mpileup.sh
--- a/phe_samtools_mpileup.sh	Mon Dec 21 09:00:43 2015 -0500
+++ b/phe_samtools_mpileup.sh	Mon Dec 21 10:17:45 2015 -0500
@@ -8,14 +8,7 @@
 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