Notice:
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.
Attention:
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

GATK3.8 vs GATK4 HaplotypeCaller

Hello, maybe I'm asking a naive question and maybe it has been answered somewhere else, but as the title states are there differences in the algorithm of the HaplotypeCaller between GATK3.8 release and GATK4?
I'm calling variants in two exomes, using the same bam files as input of the variant caller, and I tried to compare variants at the end of the pipeline. I found that GATK4 calls a slightly higher number of variants than GATK3.8 and that this one in the final step step (after filtering and selecting variants) retains variants filtered away from the GATK4 HC, is this expected or do I have to go trough my pipeline and check for errors?
Thank you

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @RobSir
    Hi,

    I think there may be minor differences in edge cases (low quality or low coverage areas). But, the outputs should be functionally equivalent. What exactly is "slightly higher"? Do you have exact numbers? What kind of differences are there after filtering?

    Thanks,
    Sheila

Sign In or Register to comment.