Mutect2 resources guide

Posted by shlee on 31 Jan 2018 (1)

A new tutorial for somatic calling

We have a new tutorial, Tutorial#11136, that outlines how to call somatic short variants, i.e. SNVs and indels, with GATK4 Mutect2. The tutorial provides small example data to follow along with.

Mutect2-compatible germline resources

Full-length Mutect2-compatible human germline resources are available on our [FTP server]( and at gs://gatk-best-practices/. The resources are simplified from the gnomAD resource and retain population allele frequencies. Mutect2 and GetPileupSummaries are the two tools in the workflow that each require a germline resource.

Working WDL scripts

If you want to run the Somatic Short Variant Discovery Best Practices workflow using WDL, be sure to check out the official Mutect2 WDL script in the gatk-workflows repository. @bshifaw and other engineers optimize the scripts in the repository to run efficiently in the cloud. Furthermore, the scripts come with example JSON format inputs files filled out with publically-accessible cloud data.

For other Mutect2-related scripts, e.g. towards panel of normals generation, check out the gatk repository's scripts/mutect2_wdl directory. Our developers update these scripts on a continual basis.

For background information

If you are new to somatic calling, be sure to read Article#11127. It gives an overview of what traditional somatic calling entails. For one, somatic calling is NOT just a difference between two callsets in that germline variant sites are excluded from consideration.

For those switching from GATK3 MuTect2, Blog#10911 will bring you up to speed on the differences.

An off-label tutorial for simple difference calling

If you are interested in simply calling differences between two samples, Blog#11315 outlines an off-label two-pass Mutect2 workflow. Off-label means the workflow is not a part of the Best Practices and is therefore unsupported. However, if given enough community interest, we may be convinced to further flesh out the workflow. Please do post to the forum to express interest.

Return to top

Wed 31 Jan 2018

- Recent posts

- Upcoming events

See Events calendar for full list and dates

- Recent events

See Events calendar for full list and dates

- Follow us on Twitter

GATK Dev Team


See also the #GATK blog post by co-author Yossi Farjoun for an overview
17 Jul 18
RT @BioCodePapers: GATK PathSeq: A customizable computational tool for the discovery and identification of microbial sequences in libraries…
10 Jul 18
RT @xdopazo: Still some vacancies in the GATK workshop in Seville do not miss it! @gatk_dev @ClinicalBioinfo @FProg…
9 Jul 18
Holiday notice: The #GATK forum is on break today as we celebrate US Independence Day. Barring any alien invasion o…
4 Jul 18
@StevenNHart @delagoya Thanks for the suggestion, will look into this.
27 Jun 18

- Our favorite tweets from others

Very productive week in Cambridge thanks to @gatk_dev , your trainers Eric, Soo Hee, Kate and Takuto were highly or…
19 Jul 18
Cambridge GATK4 variant discovery workshop day 2 is underway! The Broad team are doing an excellent job making thi…
17 Jul 18
These data are a useful benchmarking resource for any variant caller - @lh3lh3 performed a heroic number of compari…
16 Jul 18
Davide Sampietro presenting our work on an #FPGA implementation of the #pairhmm step of the @gatk_dev pipeline by…
11 Jul 18
@delagoya @gatk_dev Might want to try the builder design pattern for docker.
26 Jun 18

See more of our favorite tweets...