I am trying to perform an imputation on a VCF file that I have but using my own reference panel. I am getting confused with the parameters though. Here is what I understand:
-g is my vcf file that I am trying to impute -known_haps_g is the hap file of the file I am planning to impute in case I do not provide it in -g -m is the recombination file as per the sample provided by impute2 -h the haplotypes for the reference file -l the legend file of the reference file
Is that correct?