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Enhancements to hgvs to vcf conversion resiliency #549

@h-joshi

Description

@h-joshi

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)

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