Can the Gnomad PCA Be Used for Exomes?

Hail Query & hailctl
1

I have exome vcf data and would like to use the PCA from gnomad to determine the ancestries of my samples?

The following blog discussing PCA says:

If your dataset is missing large numbers of the variants with gnomAD PCA loadings, it will produce unreliable results.

Does that mean exome data cannot be used? Will also ask this question on the gnomAD forum in case it is something they would know.

Thank you

2

Hey @beneopp ! We (Hail team) lack the expertise to answer this question. Could you repost this at the gnomAD forum? https://discuss.gnomad.broadinstitute.org