Mercurial > repos > ulfschaefer > phephenix
changeset 5:e2ee6acf8752 draft
Uploaded
| author | ulfschaefer |
|---|---|
| date | Thu, 16 Jun 2016 06:39:37 -0400 |
| parents | 7ccbcc8608fa |
| children | 74f595df6e51 |
| files | filter_vcf.sh |
| diffstat | 1 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- a/filter_vcf.sh Thu Jun 16 06:39:26 2016 -0400 +++ b/filter_vcf.sh Thu Jun 16 06:39:37 2016 -0400 @@ -6,13 +6,15 @@ shift VCF=$1 shift +REF=$1 +shift ONLYGOOD=$1 shift FILTERS=$@ FILTERS=$(echo -n $FILTERS | sed 's/ /,/g') -CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT" +CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT --reference $REF" if [ $ONLYGOOD != "NOTTHERE" ]; then CMD="$CMD --only-good"