Mercurial > repos > biomonika > linkyx

annotate LINKYX_mpileup_wrapper.sh @ 13:ef5c8ed727b0

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
toolshed12
author biomonika <biomonika@psu.edu>
date Wed, 10 Sep 2014 10:49:56 -0400
parents 1955f03f092e
children ea52ef8d7f3a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
1 #!/bin/bash
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
2 results=$1;
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
3 bam_file=$2;
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
4 reference=$3;
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
5
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
6 sorted_bam=${bam_file}_sorted
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
7
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
8 #LINKYX_PATH set during toolshed installation
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
9
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
10 samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
11
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
parents:
diff changeset
12 #samtools mpileup -uf $reference $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt