Conversion not returning all variant entries about vcf2fhir HOT 4 CLOSED

Hi @clake-deloitte , generally this is because the VCF rows in question are meeting some exclusion criterion (described here). A nice way to see why a given row isn't converting is to enable and check the invalid record log (described here). Can you give that a try?

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Hi, yes this is actually very helpful. However, I'd like to have all the variants kept - and it seems that all of the variant entries have the same error (which is why they're being dropped):

2023-05-02 16:21:28,091 - vcf2fhir.invalidrecord - DEBUG - Reason: VCF FORMAT.GT is in ['0/0','0|0','0'], Record: Record(CHROM=1, POS=55416, REF=G, ALT=[A]), considered sample: CallData(GT=0|0, DS=0.05, GL=[-0.48, -0.48, -0.48])

Is there any way to forego this dropping of these variants at all, short of modifying the VCFs directly? Thanks!

from vcf2fhir.

Hi @clake-deloitte, unfortunately there is no way to forego the dropping of the variants without a code change (or changing the VCFs as you mention). If you do edit the code, there might be other consequences that need to be tested - for instance, calculating allelic state relies on genotype.

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Ok, no problem, thank you for the information!

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