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.
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.
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!
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 for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
In term of algorithms, what is the difference between haplotypecaller and unifiedgenotyper
bbsunchen
USAMember ✭
Under every poster of GATK asking which is better, HC or UG, Geraldine always said HC.
So Is there any documents talking about the detail algorithms HC and UG are using, so that I can get a clear idea why HC is better?
Thanks.
Tagged:
Answers
@bbsunchen
Hi,
The HaplotypeCaller algorithm is documented in these four documents:
https://www.broadinstitute.org/gatk/guide/article?id=4147
https://www.broadinstitute.org/gatk/guide/article?id=4146
https://www.broadinstitute.org/gatk/guide/article?id=4441
https://www.broadinstitute.org/gatk/guide/article?id=4442
-Sheila
P.S. The major difference between HaplotypeCaller and UnifiedGenotyper is in the first 3 steps. The math for genotyping is the same between the two (last document).