[REQUEST]: hvcf2gvcf for a specific taxa list

[jesse-hill]

Description

I'm currently trying to get SNPs from my imputed hVCFs from the ropebwt imputation pipeline. I've noticed that hvcf2gvcf first exports all the PHG founder lines before exporting the lines I've imputed. Sometimes, the export of the founder lines stalls and never fully exports the gvcfs, but that's a separate issue. I don't necessarily need the founder line gvcfs, so would it be possible to add on a flag to hvcf2gvcf to give it a taxa list of just the lines I wanted exported? Especially for future use, if I decide I want to impute additional lines, it would save a bit of time just exporting the lines I needed, versus everything in tiledb. Maybe even a flag that says don't export the founders would be useful.

I'm using phg v2 version 2.4.45.200.

Alternatives

No response

Additional Context

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[mtkelleher]

Wanted to follow this question. I assumed the gvcfs created in hvcf2gvcf were dependent on the parent gvcf files being in the same output directory, but I could be wrong. I noticed that if the gvcfs, at least in the case of copying the parent gvcfs created by create-maf-vcf, are already in the output directory, then they are not generated.