Mercurial > repos > biomonika > monika_mpileup

changeset 24:48b51529b1b8 draft

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Uploaded
author biomonika
date Thu, 14 Aug 2014 11:05:10 -0400
parents ac995857db31
children 09080c07ca04
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	Thu Aug 14 11:05:10 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 $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt
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