Have used Impute2 for imputation with the provided reference panels (mostly 1k) and that has always worked well.
For a certain project, am considering the feasibility of using a "custom" reference panel for a set of samples (~200) that are from a population, which went through a severe bottleneck. I have vcf files from a consortium of sorts that would need conversion to the reference panel format.
1. Are there any existing options/tools to generate the recombination map file to work with my vcf (which I plan to convert to legend and haps format for Impute2)
2. Been trying to search for thoughts/experiences if this "custom" reference panel approach has been tried and the pros and cons that I might be overlooking in my excitement.
Thanks for your insight!
