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quinlan-lab / vcf2db

create a gemini-compatible database from a VCF
MIT License
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Support more dbNSFP fields annotated by VEP #25

Open a113n opened 7 years ago

a113n commented 7 years ago

With reference to the PR in brentp/geneimpacts#12

brentp commented 7 years ago

sorry for the delay in answering.

@a113n thanks for these changes, but, I won't accept until the arey are optional. This adds a bunch of fields to the database even when those fields might not be present in the VCF.

The advantage of this over the existing method that @matthdsm mentions is that these are typed values whereas the current method sets all VEP extra's to TEXT.

I think a better strategy might be to add a --numerics argument that will accept a list of column names and force all of those to be sql.Float().