The map file


The map file has the format as the PLINK map file, which has four columns:
Chromosome
Marker ID
Genetic Position
Physical Position

Because SeqSIMLA reads a set of reference sequences, all markers are assumed to be on the same chromosome. The chromosome is always 1. Marker IDs are labeled as snp1, snp2,..., snpM. The genetic positions are calculated based on the recombination fractions using Haldane's map function. The physical positions are approximated by taking the genetic positions multiplied by 106.