GOLD - Haplotype File Format

Haplotype files should describe one haplotype per line in the following format:

<name> <state1> ... <stateN>

Where <name> is a text label (no spaces) for this haplotype, and <state> is the observed allele at each marker locus in this haplotype. States should be encoded numerically, and the missing value code is 0 (zero).

An example haplotype file, with 3 haplotypes genotyped at seven SNP markers would be:

  HAPLO_1   1 1 1 2 1 2 1
  HAPLO_2   1 2 2 1 2 1 2
  HAPLO_3   2 1 1 2 1 0 0