search

rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
Other
189 stars 55 forks source link

Variants included in the mask #477

Open scienception opened 11 months ago

scienception commented 11 months ago

Is it possible to get the number of variants for each person that were included within the given mask? Like a subset of the output of --write-mask-snplist, but for each person. Not in general. I'm interested in getting a "burden" of variants for each person.

scienception commented 11 months ago

I know "sum" mask does this, but I don't know where this info is stored since it doesn't write any PLINK files.

joellembatchou commented 11 months ago

Hi,

This is not possible in REGENIE; you can use the mask snplist file & manually load the genotype matrix subset to your gene of interest in like R to get your desired result.

Cheers, Joelle