Mercurial > repos > biomonika > monika_mpileup

changeset 14:adcb5eed5795 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 16:38:21 -0400
parents 88acb2da975c
children 7f57b3213b2b
files LINKYX_mpileup_wrapper.sh
diffstat 1 files changed, 7 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LINKYX_mpileup_wrapper.sh	Wed Aug 13 16:38:21 2014 -0400
@@ -0,0 +1,7 @@
+#!/bin/bash
+results=$1;
+bam_file=$2;
+reference=$3;
+
+#samtools mpileup -uf $reference $2 >$results;
+samtools mpileup -uf $reference $2 | bcftools view -p 0.85 -cgv - | vcfutils.pl varFilter >$results 2>&1
\ No newline at end of file