Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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 get best performance in Merging 6K samples using CombineGVCFs and GenotypeGVCFs (GATK 4.0.9)

I am looking for the right practices in merging 6K samples using CombineGVCFs and GenotypeGVCFs to get the best performance. I don't see Spark appended Suffix for these, does that mean these methods can't make use of spark?

I also came across some old threads on plans in bringing tileDB in 4.0 version, which could improve the performance. How can I make use of tileDB?

PS: I generated the gvcfs using HaplotypeCallerSpark in gatk4


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