Can the Gnomad PCA Be Used for Exomes?

[iris-garden]

Note

The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.

(Dec 29, 2023 at 15:50) beneopp said:

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

(Jan 02, 2024 at 14:31) danking said:

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