Mercurial > repos > biomonika > monika_mpileup

changeset 9:f63302fe8f0c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author biomonika
date Wed, 13 Aug 2014 16:33:50 -0400
parents fa5992807f7a
children 188b16f2d6f8
files LINKYX_mpileup_wrapper.sh
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/LINKYX_mpileup_wrapper.sh	Wed Aug 13 16:11:02 2014 -0400
+++ b/LINKYX_mpileup_wrapper.sh	Wed Aug 13 16:33:50 2014 -0400
@@ -3,4 +3,5 @@
 bam_file=$2;
 reference=$3;
 
-samtools mpileup -uf $reference $2 >$results;
\ No newline at end of file
+#samtools mpileup -uf $reference $2 >$results;
+samtools mpileup -uf $reference $2 | bcftools view -p 0.85 -cgv - | vcfutils.pl varFilter >$results
\ No newline at end of file