I am hoping to use vcftools to convert my phased vcf file (from beagle, where the genotypes are coded as reference and alternate - 0 and 1) into the format required for LDhat.
This is possible using the —ldhat flags, however I want to include all of my “chromosomes” (scaffolds) of which there are around 6000. Do I need to include a list of all 6000 chromosomes? Or how can I use vcftools to convert to LDhat format in my case?
Also, is it possible to convert the 0s and 1s to the actual nucleotides, as required for LDhat?
Many thanks for any help or suggestions,