Seyoon Ko

https://zzz.bwh.harvard.edu/plink/summary.shtml > Linkage disequilibrium based SNP pruning Sometimes it is useful to generate a pruned subset of SNPs that are in approximate linkage equilibrium with each other. This can be...

Source code for PLINK 1.07 is much more readable: https://github.com/poulson/plink/blob/master/genome.cpp#L1172

The current implementation of GRMs looks very memory-consuming for kinship pruning. Is there other use of GRMs other than pruning?

GRM creating the whole n x n matrix as an output. Isn't a sparse matrix or a graph data structure enough as input for kinship pruning?

Oh, I got it. The destination file (default argument is used) is unchanged for each filtering. Maybe we can change the default name each time the `filter` function is called?

The issue is that indexing on SnpArray does not return SubArray{SnpArray}, but SubArray{UInt8,2}. I can think of two options to resolve this: change indexing on SnpArray to return a SubArray{SnpArray},...