Mercurial > repos > ulfschaefer > phe_samtools_mpileup

changeset 10:f78ed0f61f52 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ulfschaefer
date Mon, 21 Dec 2015 10:17:45 -0500
parents 17996fd454c6
children 714a4c13d64c
files phe_samtools_mpileup.sh
diffstat 1 files changed, 0 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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