How to use Plink2 files including multiallelic file

broadinstitute / tensorqtl

Ultrafast GPU-enabled QTL mapper

BSD 3-Clause "New" or "Revised" License

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Closed kendaida closed 2 years ago

kendaida commented 2 years ago

Hi, I would like to use plink2 pfiles including multialleclic variants. I installed pgenlib but it could not run at 'genotypeio.PlinkReader".

pr = genotypeio.PlinkReader(pfile_prefix_path)

I think plink bfile can not include multiallelic variants. Would you tell me how to solove it?

francois-a commented 2 years ago

Hi, Multi-allelic variants are not fully supported in the API. I recommend splitting multiallelic sites instead, using bcftools norm for example.

kendaida commented 2 years ago

I got it. I appreciate you.