A hap file organizes SNP matrix of a population with phased haplotypes in a genomic region. We assume that all sites are biallelic and polymorphic in the sample. Thus, our input is in the form of a binary SNP matrix with each columns corresponding to a haplotype and each row to a mutation, and entries corresponding to the allelic state, with 0 denoting the ancestral allele, and 1 denoting the derived allele. The first column is corresponding to the position of mutations.
| #Position(bp) | Haplotype 1A | Haplotype 1B | Haplotype 2A | Haplotype 2B | ... |
|---|---|---|---|---|---|
| 291 | 1 | 1 | 0 | 1 | ... |
| 626 | 0 | 0 | 0 | 1 | ... |
| 721 | 0 | 1 | 0 | 0 | ... |
| 1208 | 1 | 1 | 0 | 0 | ... |
| ... | ... | ... | ... | ... | ... |
- TAB separated
- No Header
- Comment by #
- Positions must be sorted numerically, in increasing order