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!
Is there a paper describing the »Haplotype Caller algorithm?
cafetera
Universite de MontrealMember ✭
Hi,
I'd like to ask you if there is a paper describing the Haplotype Caller algorithm, if you could please send me the reference. I have tried to find it, but I only found the paper on GATK which is great, but it doesn't describe in detail the Haplotype Caller algorithm.
thank you,
Tagged:
Answers
We are working on a manuscript to publish the Hc algorithm. In the meantime, check out the HC documentation here: https://www.broadinstitute.org/gatk/guide/article?id=4148
Has the paper published?
Not yet, finishing up the last details.
Has this paper been published. If so could you possibly point me to it please.
No, sorry. We decided to add an analysis to make it more complete, and that's still in progress.
Is there anywhere that you have got more of a detailed explanation of how HC calculates activity profiles and performs smoothing. I have read the explanation here https://www.broadinstitute.org/gatk/guide/article?id=4147 but I just wanted to know a little more of the mathematical detail.
@kjpr
Hi,
No there is no more detailed document explaining the active region determination. The best thing is to look at the code.
-Sheila
Ok thanks I look forward to when the HC paper comes out.
Has the paper about algorithms used in Haplotype Caller published?If so could you give me a reference please.Thanks in advance.
@jesson
Hi,
No, there is no paper. You can either look at the code and/or reference the GATK forum.
-Sheila
Ok, thanks for the kind reply.
Hello,
Could you please help me with the paper, if it had been published?
Thanks
@KushalD
Hi,
Here it is.
-Sheila