These are scripts for inferring constraint for population genomic data as done in Schrider and Kern 20151. Methods are adapted for working with maize hapmap data, which has more problems with alignment than human 1000 genomes data.
1 Schrider, D. R. & Kern, A. D. Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain. Genome Biol. Evol. 7, 3511–3528 (2015).