To be precise. I am doing a gene based test using bayesian approach. For which there are certain prerequisite files, one is the .hap file.
It should contain the details on,
1. freq. of second/minor allele
2. base pair position of the corresponding SNP
3. along with the haplotype details (for the allele combination)
4. and it is for specific population (say for eg., CEU)
One option that i can think of is obviously the 1000g data from the hapmap (VCF data). But got no idea of how to proceed on further (with plink or with any other packages). Any suggestions will be of great help.
Thanks a bunch