We have a Vcf file containing the variants from a haploid species. We need to carry out PCA analysis on these variants but most are linked. How can we select a set of unlinked variants? PLINK is set up to do on diploid genotypes. How does one work with haploid genotypes if one uses PLINK?
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wrab425 •
1 answer
PLINK's --indep-pairwise command for selecting approximately-unlinked variants should have no problem with haploid data. However, you'll want to perform the actual PCA with another script/tool, since the variance-normalized similarity formula used by PLINK --pca only works properly for diploid data.
(Edit: on second thought, dividing the eigenvalues by 2 at the end should be enough to correct for the haploid/diploid variance difference.)
No, because --pca uses variance-standardized genotype values.
Meanwhile, plink 2.0 --pca should correct the eigenvalues for you.
I have run all of the commands in the pca pipeline and it all runs beautifully and gives what look like excellent results. I get the same results with or without the --chr-set -3 flag however and I am unsure what is going on. I have looked through all of the output files and am not sure whether it has correctly taken into account ploidy. Is there a way that I could check that my output is not corrupted? Is there a small diploid vcf around that I could use to check what has gone on? Thanks
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