Would it be possible to directly create PLINK2 pgen/pvar/psam from a MatrixTable? The function
export_plink exports only PLINK1 BED/BIM/FAM files.
We do not currently support this. Is there a PLINK1 to PLINK2 conversion tool you could use?
Right now I write the MT as a VCF and then convert it with PLINK2 to pgen/pvar/psam which works fine, but it just adds an extra step to the pipeline.
I was looking at the PLINK2 documentation linked here, and it looks like you can use BED/BIM/FAM as inputs to plink2.
Is there something that you need on top of what export_plink would output?
At the end of the day I just would like to have the pgen/pvar/psam formats directly via HAIL, so something like a export_plink2 function. There is no need for me to do anything via PLINK1/PLINK2, just some downstream tools need the pgen/pvar/psam format.