Entering edit mode
3.0 years ago
Jenish
▴
20
Does PRSice-2 support a base tile that has chromosome number/name and chromosome position instead of reference SNP ID in the base file?
I'm trying to calculate PRS scores using a weights file from the PGS catalog with ~6 million variants. The file has only chr name and chr positions. Does PRSice-2 support such files as base files? Or, is there a way to get the ref SNP ID in bulk for all the ~6 million variants using the chr name and chr positions?
Thanks for the response. I had completely missed that section out. I was able to calculate the weights using the --chr-id option. Do you know of any other option that needs to be set besides these when generating PRS scores from the weight files?