casefatherduos.dat: This file contains a header line (which is not read in by the program but is useful for reminding yourself of the column order), followed by a line of data for each of the 
SNPs to be analysed (IN EXACTLY THE SAME ORDER as given in emimmarkers.dat).
The first number on each line is the numeric SNP ID (as given in emimmarkers.dat). This is followed by 7 cell counts corresponding to the number of fully genotyped case/father duos whose genotype combinations fall into the appropriate genotype categories. Note that these must not include cases and fathers who have already appeared as case/parent trios in the file caseparenttrios.dat, fathers who have already appeared in the file caseparents.dat, or cases who have already appeared in the file casemotherduos.dat (i.e. all input data files must be independent). Zero counts are allowed, although may make it more difficult to estimate certain parameter combinations.
For example, suppose that at the first SNP the genotype combinations of the father and child are
| group | father | child | count |
|---|
| 1 | 22 | 22 | 1 |
| 2 | 22 | 12 | 0 |
| 3 | 12 | 22 | 2 |
| 4 | 12 | 12 | 1 |
| 5 | 12 | 11 | 2 |
| 6 | 11 | 12 | 3 |
| 7 | 11 | 11 | 3 |
Then the line in casefatherduos.dat corresponding to this SNP would look like:
1 1 0 2 1 2 3 3
An example of casefatherduos.dat for 8 SNPs, of which the first has counts as given above, is shown below:
snp cellcount 1-7
1 1 0 2 1 2 3 3
2 0 0 1 0 5 4 1
3 0 0 0 0 0 0 11
4 0 1 0 3 0 0 7
5 0 2 1 3 1 2 2
6 0 0 0 0 2 3 6
7 0 0 0 0 0 3 8
8 1 0 1 2 2 2 5
