| Previous changeset 4:7ccbcc8608fa (2016-06-16) Next changeset 6:74f595df6e51 (2016-06-16) |
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Commit message:
Uploaded |
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modified:
filter_vcf.sh |
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| diff -r 7ccbcc8608fa -r e2ee6acf8752 filter_vcf.sh --- a/filter_vcf.sh Thu Jun 16 06:39:26 2016 -0400 +++ b/filter_vcf.sh Thu Jun 16 06:39:37 2016 -0400 |
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| @@ -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" |