I am looking for a way to genotype a specific set of variants/sites in GATK188.8.131.52. In previous versions it was possible to provide a sites-only vcf (back then to UnifiedGenotyper) to have all these sites genotyped. However, I cannot find this option in genotypeGVCFs.
Background: I have populations/species with highly stratified allele frequencies, and I want to genotype these separately to not bias the genotypes by the allele frequencies in the entire set of individuals. To still get the same sites called, however, I have to provide a list of sites/variants.
Thanks a lot for any insights!
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