How to predict sample ethnicty from a VCF using 1000G or gnomAD ?

Question

[Nicolas Rosewick]

Hi,

There were already some discussion started to predict sample ethnicity from population genetic studies (1000G, gnomAD) e.g. A: How to predict individual ethnicity information by using hapmap data who used the PC from 1000G to create a predicitve model.

However I was wondering if there are already tools/R packages that take as input a vcf file and outputs the ethnicity of the samples ?

Thanks

Answer 1

[WouterDeCoster]

Not R, but I would suggest taking a look at peddy.

[Nicolas Rosewick]

Thank you @WouterDeCoster . Exactly what I wanted :)