Mercurial > repos > nicolas > oghma
annotate beagle_phase.sh @ 103:e7115e44d8d8 draft default tip
Uploaded
| author | nicolas |
|---|---|
| date | Mon, 31 Oct 2016 07:20:49 -0400 |
| parents | 10afd4b2847b |
| children |
| rev | line source |
|---|---|
| 20 | 1 #!/bin/bash |
| 2 | |
| 25 | 3 # variable affectation |
| 20 | 4 vcf_input=$1 |
| 5 out="out_phased" | |
| 6 | |
| 25 | 7 # create temporary directory |
| 20 | 8 directory=`dirname $0` |
| 9 mkdir tmpdir$$ | |
| 10 cp -rf $vcf_input tmpdir$$/input.vcf | |
| 25 | 11 # launch beagle |
| 20 | 12 java -jar $directory/beagle.jar gt=$vcf_input out=$out |
| 25 | 13 # remove temporary directory |
| 20 | 14 rm -rf tmpdir$$ |