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.
Should I use UnifiedGenotyper or HaplotypeCaller to call variants on my data?
The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, its ability to call indels is far superior, and it is now capable of calling non-diploid samples. It also comprises several unique functionalities such as the reference confidence model (which enables efficient and incremental variant discovery on ridiculously large cohorts) and special settings for RNAseq data.
As of GATK version 3.3, we recommend using HaplotypeCaller in all cases, with no exceptions.
Caveats for older versions
If you are limited to older versions for project continuity, you may opt to use UnifiedGenotyper in the following cases:
- If you are working with non-diploid organisms (UG can handle different levels of ploidy while older versions of HC cannot)
- If you are working with pooled samples (also due to the HC’s limitation regarding ploidy)
- If you want to analyze more than 100 samples at a time (for performance reasons) (versions 2.x)