Kinship matrix generation

[Thatguy027]

Should we be using a kinship matrix built on the entire SNV set?

I think we should be running LD pruning prior to generating a kinship matrix to not inflate sample relatedness.

Does the A.mat function of rrBLUP, take marker LD into consideration when making the kinship matrix?

[Thatguy027]

lets also test kinship matrices generated using this popkin package