Mercurial > repos > nicolas > oghma

annotate beagle_phase.sh @ 23:6a75b93ba5f2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author nicolas
date Fri, 21 Oct 2016 10:35:32 -0400
parents f9a3d6a36ca5
children 10afd4b2847b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
1 #!/bin/bash
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
2
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
3
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
4 vcf_input=$1
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
5 out="out_phased"
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
6
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
7 directory=`dirname $0`
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
8
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
9 mkdir tmpdir$$
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
10
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
11 cp -rf $vcf_input tmpdir$$/input.vcf
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
12
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
13
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
14 java -jar $directory/beagle.jar gt=$vcf_input out=$out
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
15
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
16
f9a3d6a36ca5 Uploaded
nicolas
parents:
diff changeset
17 rm -rf tmpdir$$