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PacificBiosciences / HiPhase

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
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Feature request: haplotag in phased VCF files #25

Closed andyjslee closed 9 months ago

andyjslee commented 9 months ago

Thank you for developing such a useful tool! Would it be possible to include the haplotag information (stored in the --haplotag-file file) in the phased VCF files? HiPhase currently only outputs PS (phase set identifier) in the phased VCF files.

holtjma commented 9 months ago

Hi @andyjslee,

If you're referring to the haplotag column, that is implicitly encoded in the VCF file. For example, if GT=1|0, it indicates that the ALT allele is in haplotype 1 and the REF allele is in haplotype 2. Are you referring to that or something else?

Matt

andyjslee commented 9 months ago

Thank you for your quick response. You are right. I'll close this issue/feature request. Thank you!