search

broadinstitute / tensorqtl

Ultrafast GPU-enabled QTL mapper
BSD 3-Clause "New" or "Revised" License
162 stars 52 forks source link

Which is the effect allele? #72

Closed ariadnacilleros closed 2 years ago

ariadnacilleros commented 2 years ago

Hi,

I have been conducting some mQTLs mapping using the nominal approach from Tensor. But I have question, which is the allele tested for the effect, p-value and standard error reported in the results?

Thanks!

Ariadna

francois-a commented 2 years ago

Hi, the effect allele is always the ALT allele.

Hiroaki-S-Ri commented 2 years ago

Hi, is the ALT allele minor allele of plink bed?

francois-a commented 2 years ago

Hi, tensorQTL requires alleles to be encoded as REF/ALT. The default encoding of alleles as minor/major is a common issue with PLINK 1, see here and here.