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.
MUTECT2 vs MUTECT1
Hello,
We are using MUTECT to call somatic variants in cancer
thus far we were using MUTECT1
It works fast, however it does not call indels.
New MUTECT2 in GATK 3.5 calls both point mutations and indels.
The only problem that we have with Mutect2 is that it is much slower (20-50 times) than Mutect1.
We tried to parallelize it, but it is still super slow.
Maybe you could help us with this issue?
Thanks in advance
Tagged:
Best Answer
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Sheila
Broad Institute admin
@Serguei
Hi,Yes, MuTect2 is slower that MuTect1 because of the reassembly step. Have a look at this thread for more information. Unfortunately, we really don't have any recommendations for speeding it up now. You can also look into using WDL.
-Sheila
Answers
@Serguei
Hi,
Yes, MuTect2 is slower that MuTect1 because of the reassembly step. Have a look at this thread for more information. Unfortunately, we really don't have any recommendations for speeding it up now. You can also look into using WDL.
-Sheila