conmotherduos.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 control/mother duos whose genotype combinations fall into the appropriate genotype categories. Note that by controls we mean individuals of unknown disease status, or (provided the disease is rare) individuals who are known to be disease-free. This must not include individuals who have already appeared in any other input files (i.e. all input data files must be independent).
For example, suppose that at the first SNP the genotype combinations of the mother and child are
| group | mother | child | count |
|---|
| 1 | 22 | 22 | 0 |
| 2 | 22 | 12 | 0 |
| 3 | 12 | 22 | 1 |
| 4 | 12 | 12 | 1 |
| 5 | 12 | 11 | 2 |
| 6 | 11 | 12 | 2 |
| 7 | 11 | 11 | 21 |
Then the line in conmotherduos.dat corresponding to this SNP would look like:
1 0 0 1 1 2 2 21
An example of conmotherduos.dat for 8 SNPs, of which the first has counts as given above, is shown below:
snp cellcount 1-7
1 0 0 1 1 2 2 21
2 0 0 0 0 3 7 16
3 0 0 0 1 2 2 20
4 0 0 0 2 4 2 16
5 0 0 2 1 2 1 19
6 0 0 0 1 2 0 23
7 0 0 0 3 5 5 13
8 0 0 0 1 1 3 21
