GOLD - HaploXT Documentation

Input

haploxt takes as input a set of haplotypes, which should be stored in a file named HAPLO.LST (such as that generated by collect-simwalk2).

Output

haploxt generates as output a file summarising observed linkage disequilibrium (LD.XT). Disequilibrium statistics are also output to the screen. The LD.XT can be used as input to the graphical interface. A typical series of commands would be:

> setup-simwalk2 pped.dat mmap.dat
> simwalk2
> collect-simwalk2
> haploxt

Options

Individual marker-by-marker contingency tables can be viewed with the verbose option (-v). A quality threshold can be specified (-qNN) so that haplotypes typed at less than NN% of loci are ignored. Rare microsatellite alleles below some frequency FF% can be pooled for analysis (-pFF).