Getting genotype type counts in sliding windows across genome
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!
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David Minkley •
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