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blachlylab / vcf_atomizer

Parses a VCF file into line-delimited json
MIT License
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Suggestions for standard VCF annotated fields to parse? #2

Open charlesgregory opened 3 years ago

charlesgregory commented 3 years ago

@jblachly any suggestions? I feel that our atomizer should be able to parse out information/annotations so that it is compatible with many different annotated vcfs. I assume we should be able to parse clinvar, snpeff, and vep annotations?

charlesgregory commented 3 years ago

We already support parsing the ANN field. The other parsable INFO fields I am aware of are: vep, CSQ (which is also vep format?), LOF, NMD (also LOF format)

jblachly commented 3 years ago

if you had to pick one to parse for maximum / widespread usage, I would pick VEP