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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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Something wrong? #17

Closed ryuzheng closed 7 years ago

ryuzheng commented 7 years ago

Hi,

Your jobs are awesome! I think it would be very useful for us. But as I look at the example clinvar.tsv.gz file and the clinvar_example_750_rows.tsv file, I find a mistake.

chrom pos ref alt mut measureset_id symbol clinical_significance pathogenic benign conflicted review_status gold_stars hgvs_c hgvs_p all_submitters all_traits all_pmids inheritance_modes age_of_onset prevalence disease_mechanism origin xrefs
1 949523 C T ALT 183381 ISG15 Pathogenic 1 0 0 no assertion criteria provided 0 NM_005101.3:c.163C>T NP_005092.1:p.Gln55Ter OMIM Immunodeficiency 38 with basal ganglia calcification;IMMUNODEFICIENCY 38 WITH BASAL GANGLIA CALCIFICATION 25307056 Childhood <1 / 1 000 000 germline MedGen:CN221808;OMIM:616126;Orphanet:319563
1 949696 C CG ALT 161455 ISG15 Pathogenic 1 0 0 no assertion criteria provided 0 NM_005101.3:c.339dupG NP_005092.1:p.Leu114Alafs OMIM Immunodeficiency 38 with basal ganglia calcification;IMMUNODEFICIENCY 38 WITH BASAL GANGLIA CALCIFICATION 1,22859821,25307056 Childhood <1 / 1 000 000 germline MedGen:CN221808;OMIM:616126;Orphanet:319563

At this sheet, the second row of the result, there is a "1" in the all_pmids column, are there a mistake of the program?