rehh

Want to use rehh to make bifurcation diagrams. However, it requires screwy format types. I will try to coerce our data into.

Requires a .hap file, which is a space-delimited file, with each line representing a haplotype (the first line being the haplotype ID).

1 2 2 2 1 1 2 1 2 2
2 2 1 1 1 2 2 1 2 1
3 1 1 1 1 1 2 2 2 1

So in the above example, this represents three haplotypes / chromosomes / haploid individuals, with 9 markers each.

The space-delimited map file (ends in .inp) is similar to the map file required by selscan. First column is locusID, second column is chromosome number, third column is genetic or physical distance, ancestral allele (1 or 2), derived allele (2 or 1). No header in case of either file. Example below (not related to the .hap file example above).

F0100190 1 113642 1 2
F0100220 1 244699 1 2
F0100250 1 369419 1 2
F0100270 1 447278 1 2
F0100280 1 487654 1 2
F0100290 1 524507 2 1