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Enhancements to hgvs to vcf conversion resiliency #549

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h-joshi opened this issue Jun 17, 2022 · 0 comments

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h-joshi commented Jun 17, 2022

Is your feature request related to a problem? Please describe.

Converting from HGVS to VCF is always a challenge

Semi - regularly updated transcript versions result in difficulties during conversion e.g. NM_00003.2 vs NM_00003.3
For variants failing conversion, hgvs to vcf script currently halts

Describe the solution you'd like
Enhance hgvs to vcf feature such that

Optionally transcript version (in input) can be ignored. The output VCF INFO field can specify which version was used during conversion
Provide a flag to continue processing irrespective of error. The output VCF should contain the error (whether it's an invalid hgvs entry, one that cannot be processed due to whatever reason)

h-joshi added the enhancement label

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