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broadinstitute / tensorqtl

Ultrafast GPU-enabled QTL mapper
BSD 3-Clause "New" or "Revised" License
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recommendations for lcWGS derived genotype likelihoods #169

Open laurahspencer opened 6 days ago

laurahspencer commented 6 days ago

Hello! Is it possible to use tensorqtl to perform QTL analyses with genotype likelihoods derived from low-coverage whole genome sequencing data, instead of hard-called genotypes?

Thanks for any guidance you can provide!

francois-a commented 6 days ago

Hi, definitely. The genotype input is flexible as long as it's in a compatible format. If the likelihoods are stored as dosages in PLINK pgen you can pass the --dosages flag to read those instead of the hard calls.