Closed dvg-p4 closed 1 year ago
So this needs to be a two-step process?
If you're calculating many different scores on the same dataset, the two-step process makes sense.
If you aren't, an alternative hack that'll probably work is pointing --extract at the --score file.
I'm currently trying to use plink2 to calculate PGSs, but noticing that it takes incredibly long to calculate allele frequencies unless I set the
no-mean-imputation
flag. Since the number of variants I have in my score file is very small, and my input pgen is very large, I presume that it must be calculating allele frequencies for every variant in my pgen file. (A glance at the source code seems to suggest this is the case, though I'm not 100% sure.)