Marker set

[Thatguy027]

We need to move away from from the RADseq SNV set from Andersen 2012.

A potential approach (for single marker testing)

1. Prune markers to those that have a MAF > 0.05.
2. Prune markers to those that are present in at lease 90% of the strains.
3. LD prune - use plink to prune marker set. For every ~50Kb only keep markers that have LD less than ~0.8 r^2. Do not make incorporate a sliding window with this approach because of long LD blocks.