Mercurial > repos > biomonika > linkyx

annotate LINKYX_mpileup_wrapper.sh @ 32:cf7cd22fc5d3 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
add changeset revisions for packages
author biomonika
date Tue, 10 Feb 2015 12:09:34 -0500
parents 7997c93ee479
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
diff changeset
1 #!/bin/bash
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
diff changeset
2 results=$1;
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
diff changeset
3 bam_file=$2;
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
diff changeset
4 reference=$3;
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
diff changeset
5
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
diff changeset
6 sorted_bam=${bam_file}_sorted
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
diff changeset
7
7997c93ee479 last attempt to install perl as part of linkyx
biomonika <biomonika@psu.edu>
parents:
diff changeset
8 samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results