Fast and accurate out-of-core PCA framework for large scale biobank data

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Figure 2.
Figure 2.

Runtime and memory usage. Runtime and memory usage for calculating top K = 40 PCs in either random subsets of common SNPs (left column) for 50,000 individuals or random subsets of individuals (right column) for 3,000,000 common SNPs. We used 20 CPU threads for all programs except FlashPCA2 which does not support multithreading. Detailed commands are included in the Benchmarking section. PLINK2 (FastPCA) ran out of memory when using more than 1,000,000 SNPs.

This Article

  1. Published in Advance August 24, 2023, doi: 10.1101/gr.277525.122 Genome Res. 33: 1599-1608

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