Hello, I have a vcf file of called variants (GATK) and genotypes per individual and a text file produced from LDhelmet which contains recombination rates for windows across the genome (4 columns: chromosome, start, end, and recombination rate). I'm looking to convert this to the eigenstrat format.

I feel like I could write something ugly to (i) convert bp to cM based on the linkage information and (ii) reformat the vcf file (maybe using Mega2?), but I also think this has got to be a problem someone else has already solved much more efficiently. Thanks, and I'd appreciate any suggestions about how to best approach this problem!