6.4 Marker counts file

With the growing prevalence of genomic information and need for mixed model analyses of such data, capabilities of WOMBAT have recently been extended to perform some of the tasks required (see run options These require a file of allele counts for markers (or SNPs).

1. The ’default’ name for this input file is MarkerCounts.dat. Alternative names (up to 30 characters long) can be specified in the parameter file (see 4.7).
2. The marker counts file file must contain at least one line for each genotyped animal.
3. Information required for each animal, to be read consequentially, is comprised of :

the animal code (as in data or pedigree file) at the beginning of a new line.
the marker counts, typically 0  , 1  and 2  (through real variables are accommodated) for exactly m  markers, with m  as specified in the parameter file. These may be on the same line or extend over continuation lines.

4. Currently the only format option for MarkerCounts.dat or equivalent is a formatted file with space-separated variables (unformatted binary read or HDF5 format are planned for faster input for larger numbers of SNPs or animals).
5. NB: WOMBAT does absolutely NO checking of the contents of this file - missing counts or mono-morphic markers may create problems!