I'd like to get counts of each genotype type (homA, homR, het, plus uncalled GTs) in sliding windows across the genome. Preferably by individual in a multi-individual VCF file. I know that there are straightforward options to get total SNP counts in windows, but I can't seem to find any simple way to get at this information. My ultimate goal is to create a plot for each chromosome, for each individual, in my dataset - I'd also be interested in a way to create these plots directly.
Any help is much appreciated. Thanks!