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macarthur-lab / clinvar

This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
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Origin column #10

Closed sigven closed 8 years ago

sigven commented 8 years ago

hi,

Thanks for a very useful resource, it simplifies a lot. Would you consider adding the variant origin in the output (for annoation of 'germline,'somatic','de novo' etc.)? It is present in the variant_summary.txt.gz. I guess adding one more variable to join_data.R would work, e.g.:

colnames(txt_extract) = c('measureset_id','symbol','clinical_significance','review_status','hgvs_c','hgvs_p','origin')

best, Sigve

bw2 commented 8 years ago

Hi Sigve, Since adding another column to the output may break people's scripts, I'm hesitant to do it unless there's broader interest.

bw2 commented 8 years ago

@sigven I'm adding ModeOfInheritance and other columns as part of #11 which provide similar information as the origin column.

bw2 commented 8 years ago

origin column has been added