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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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fix filtering for --pass-only with no trio/group/sample exressions #24

Closed brentp closed 5 years ago

brentp commented 5 years ago

currently this:

slivar expr --ped $ped --js ~/bin/slivar/js/functions.js --vcf $vcf \
  --pass-only \
   --info 'INFO.gnomad_popmax_af < 0.01'

will output every variant, when the intent is obviously to output only those matching the --info filter.

slivar gnotate would be much faster for this type of query, but it should still be supported in expr.

brentp commented 5 years ago

this is fixed in pending release.