PCA with split up chromosomes

Question

[gradstudentNew]

Hi all,

Is there a way to do PCA with split up chromosome files? My files are too big to keep as a single bed/bim/fam but wanted my PCs for all chromosomes collectively instead of split up.

Thanks!

[chrchang523]

PCA should be run after you've applied a MAF filter and performed LD pruning (e.g. --indep-pairwise). If per-chromosome bed/bim/fam files are small enough to be usable at the beginning, a merged all-chromosome bed/bim/fam is almost always small enough to be usable after MAF filtering and LD pruning.

[jimhavrilla]

@chrchang523, is this true even for bgens containing 500k or more samples?