Requirements for population structure analysis

[jeromekelleher]

Basic population structure analysis is a key goal for sgkit. This is a top-level issue which tracks progress on this target, following the example of #67 for GWAS.

• Method for grouping samples into "populations" (Method for grouping samples which is understood by library functions #224)
• Running PCA on large cohorts of individuals (>10K) is essential (see PCA User Story #95, PCA #123)
• Fst (Fst function #225)
• Pairwise distance (Pairwise distance calculation #241)

@alimanfoo, is this a reasonable starting point for doing basic population structure analysis with sgkit?

[alimanfoo]

Apologies for slow response here, just to say this is a great starting point, these are our core population structure analyses.

I added some examples of how we use pairwise distance to analyse population structure here: https://github.com/pystatgen/sgkit/issues/241#issuecomment-698455959