Estimate the genomic relationship between Discovery and Target sample in PRS

Question

[landscape95]

Hi everyone,

I am trying to calculate the genomic relationship between discovery and target sample but I am not sure how to make the running time affordable for large sample size (E.g 500k individuals x 1 million SNPs).

Your help is really appreciated!

[Kevin Blighe]

Please explain better the program(s) that you are using, and providing any actual code that you have use would be helpful, too.

Answer 1

[Sam]

Given your tag and your sample size, are you trying to perform PRS analysis on UK biobank data? You can definitely run an analysis on this sample size using the common PRS software such as PRSice, lassosum and LDpred.