Mercurial > repos > ulfschaefer > phephenix
annotate filter_vcf.sh @ 15:a6079f6217f5 draft
Uploaded
| author | ulfschaefer |
|---|---|
| date | Wed, 04 May 2016 07:16:24 -0400 |
| parents | 45ff0fc972e8 |
| children | 4e64e338cc06 |
| rev | line source |
|---|---|
| 0 | 1 #!/bin/bash |
| 2 | |
| 3 echo $@ | |
| 4 | |
| 5 OUTPUT=$1 | |
| 6 shift | |
| 7 VCF=$1 | |
| 8 shift | |
| 15 | 9 ONLYGOOD=$1 |
| 10 shift | |
| 0 | 11 FILTERS=$@ |
| 12 | |
| 13 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') | |
| 14 | |
| 15 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT" | |
| 16 | |
| 15 | 17 if [ $ONLYGOOD != "NOTTHERE" ]; then |
| 18 CMD="$CMD --only-good" | |
| 19 fi | |
| 20 | |
| 0 | 21 echo "CMD: "$CMD |
| 22 eval $CMD |