If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Genotyping strategy for using UnifiedGenotyper
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.