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AstraZeneca-NGS / VarDict

VarDict
MIT License
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Better support of gVCF and VCF4.3 format for AD and AF keys #94

Closed clintval closed 5 years ago

clintval commented 5 years ago

  1. With the merge of https://github.com/AstraZeneca-NGS/VarDict/pull/58 and https://github.com/AstraZeneca-NGS/VarDict/pull/76, we now need to ensure we respect the type of the AD field when producing genome VCFs which can contain "no variant" records (no alternate alleles).

  2. I have changed the reserved INFO and FORMAT tags for AF to Number=A as per the VCF specification:

Key Number Type Description
AF A Float Allele frequency for each ALT allele in the same order as listed (estimated from primary data, not called genotypes)

Where A defines:

clintval commented 5 years ago

Hi @mjafin and @zhongwulai do you need help maintaining these scripts?

Many of my PRs are meant to keep VarDict outputs adhering to the VCF specification (currently v4.3) so I am willing.

mjafin commented 5 years ago

Hi @clintval, thanks for the note. I no longer work in AstraZeneca so have taken a step back from the Vardict duties. @pcingola and @PolinaBevad would likely be the best points of contact here