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.
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 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!

Possible to Merge Deletion and SNP event with MNP or Another Tool

I am trying to call a deletion SNP using MuTect2 from GATK4.1.2 and am following best practices. This is a common mutations in LUAD. I have attached the IGV Screenshot here. This seems unrelated to the MNP Dist length I provide to MuTect2. This is WES.

With MNP:
chr7 55242465 . GGAATTAAGA G . PASS
chr7 55242475 . GAAG CAAC . PASS

Without MNP:
BRAIN26 - With No MNP Merge
chr7 55242465 . GGAATTAAGA G . clustered_events;haplotype
chr7 55242475 . G C . clustered_events;haplotype
chr7 55242478 . G C . clustered_events;haplotype

Is there a way to have this be a single call? Or is there a way to merge the calls in post-processing?

I am aiming for an annotations which would produce L747_A750delinsP after annotation.
Tagged:

Best Answer

Answers

Sign In or Register to comment.