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.
I would like this export feature too as well as import feature. The UK BIobank is generating this format for the 500k WGS. The advantage over a standard plink file is the the INFO and filter information is available in the pgen format. Plink2 also handles multiallelic variants and longer SVs which the older plink could not handle.