Dear GATK authors,
I have two little questions about the genotyping strategy for using UnifiedGenotyper.
1) Imaging I have a list of candidate sites in hand, then I just want to use UG to genotype my individuals at these sites. Considering the sequencing coverage for each individual is low or median, will there be any difference between genotyping them on individual level and on a cohort of population level?
2) I have a list of candidate sites, including SNPs and complex indels, which were discovered by HaplotypeCaller, Then can I use UG to genotype these sites across individuals to get the correct genotypes? I know HC used a local denovo assembly to discover the variants, but I'm not sure after the variants have been discovered, whether there is any difference in genotyping result between HC and UG.