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Option to write whole VCF, not just pathogenic SNVs#33

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MattWellie merged 3 commits intomainfrom
all_vcf_write
Feb 6, 2026
Merged

Option to write whole VCF, not just pathogenic SNVs#33
MattWellie merged 3 commits intomainfrom
all_vcf_write

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Purpose

  • Current VCF-write use case is only for annotation -> PM5
  • Using Echtvar as an annotator we need a full VCF

Proposed Changes

  • adds --all_vcf CLI parameter to write an un-filtered VCF, to be used in generating an Echtvar annotation source

@MattWellie MattWellie merged commit 5f504c1 into main Feb 6, 2026
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@MattWellie MattWellie deleted the all_vcf_write branch February 6, 2026 05:08
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