Mercurial > repos > nicolas > oghma

annotate beagle_impute.sh @ 18:27fb6c2a98a3 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 06:30:52 -0400
parents
children 79abc9d00340
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
1 #!/bin/bash
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
2
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
3
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
4 vcf_input=$1
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
5 ref=$2
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
6 out="out_imputed"
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
7
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
8 directory=`dirname $0`
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
9
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
10 mkdir tmpdir$$
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
11
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
12 cp -rf $vcf_input tmpdir$$/input.vcf
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
13
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
14
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
15 java -Xmx2g -jar $directory/beagle.jar ref=$ref gt=$vcf_input out=$out
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
16
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
17
27fb6c2a98a3 Uploaded
nicolas
parents:
diff changeset
18 rm -rf tmpdir$$