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.
Which variant filering process is better for high-coverage data?
I'm currently analysing 4 high-coverage (>30X) mammalian non-human genomes.
I've implemented GATK's/Picard's dedup, realigner, fixmates, and called the variants using UnifiedGenotyper, followed by BaseRecalibrator.
Given there is no available database with variants called on other relevant samples, I'm wondering which variant filtering method is better to use:
1) Variant quality score recalibration
Thank you very much!