emimmarkers.dat: This file lists on each line (in order) a numeric SNP ID (which could correspond to SNP number or base pair position, for example) for each SNP to be analysed, together with the allele frequency for the allele denoted “2” (usually the minor allele) at each SNP.
For example, if there are 8 different SNPs to be analysed, with SNPs 1 to 8 having minor allele frequencies 0.419927, 0.28163, 0.01, 0.152068, 0.265815, 0.0991484, 0.129562 and 0.379584 respetively, emimmarkers.dat might look like:
1 0.419927
2 0.28163
3 0.01
4 0.152068
5 0.265815
6 0.0991484
7 0.129562
8 0.379584
The allele frequencies are generally only used as starting values (unless you choose the option in EMIM to fix the allele frequency at its starting value - which is NOT recommended). Therefore the allele frequencies do not have to be too accurate. An estimate from HapMap or from previous genetic studies in your population should be sufficient.
