5.8 casefathers.dat

casefathers.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 n 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 3 cell counts corresponding to the number of fully genotyped fathers of cases whose genotypes fall into the appropriate genotype categories. Note that these must not include fathers of cases already in the files caseparenttrios.dat, caseparents.dat, or casefatherduos.dat (i.e. all input data files must be independent).

For example, suppose that at the first SNP the genotypes of the fathers are

group father count
1 22 4
2 12 71
3 11 461

Then the line in casefathers.dat corresponding to this SNP would look like:

1      4 71 461

An example of casefathers.dat for 8 SNPs, of which the first has counts as given above, is shown below:

snp cellcount 1-3
1      4 71 461
2      5 64 467
3      2 27 506
4      82 239 214
5      4 55 477
6      21 162 353
7      4 62 470
8      11 110 415