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.
How to evaluate variants
I have 33 samples (VCF files) resulted from HaplotypeCaller and like to evaluate them using dbSNP as a comp to get concordance_rate, sensitivity, and specificity. One way is to evaluate each sample separately. Another approach is to combine all 33 files using "CombineGVCFs" and then evaluate one VCF file. Which of these 2 methods do you think is feasible and acceptable for variant evaluation? why? Thanks