Mercurial > repos > nicolas > oghma
annotate beagle_impute.sh @ 73:ca6af7b12073 draft
Uploaded
| author | nicolas |
|---|---|
| date | Fri, 28 Oct 2016 08:45:13 -0400 |
| parents | 79abc9d00340 |
| children |
| rev | line source |
|---|---|
| 18 | 1 #!/bin/bash |
| 2 | |
| 24 | 3 # variables affectation |
| 18 | 4 vcf_input=$1 |
| 5 ref=$2 | |
| 6 out="out_imputed" | |
| 7 | |
| 24 | 8 # create temporary directory |
| 18 | 9 directory=`dirname $0` |
| 10 mkdir tmpdir$$ | |
| 11 cp -rf $vcf_input tmpdir$$/input.vcf | |
| 24 | 12 # launch beagle |
| 18 | 13 java -Xmx2g -jar $directory/beagle.jar ref=$ref gt=$vcf_input out=$out |
| 24 | 14 # remove temporary dir |
| 18 | 15 rm -rf tmpdir$$ |