I have a multi-sample vcf that was phased using beagle. This serves as my reference. For my target, I generated a phased file from a multi-sample bed file.
For running imputations, I want to use minimac. I tried but I'm stuck! BADLY.
I generated .snps file from the .map file (for the reference, the .map was generated using plink option of vcftools, whereas the .map for target was generated using plink itself).
How do I generate .hap file input that is required for each, reference and target?
Also, it keeps saying that the markers in my snps file are not biallelic. But vcftools, when creating ped and map files, specifically output biallelic loci only.
I'm confused. Please help