RAiSD and SNP array data

[Vlatko Galic]

Hi!

I have the filtered and imputed data from genotyping ~1000 maize accessions with 600k SNP array and I was running RAiSD. Although the results seem promising, I'm concerned about the ascertainment bias in SNP array as compared to sequencing data, with underrepresentation of rare variants.

This certainly affects the muSFS, but are my results still valid computation-wise?

Is it even advisable to use RAiSD with array SNPs?

Thanks!

[N.Alachiotis]

You can find a response to this question here: https://github.com/alachins/raisd/issues/23