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.
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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 variant calling without a known intervals list

Hi Sheila,
I am analyzing somatic variants in exome sequencing data from paired tumor/normal samples for which the intervals list is unknown. I have been using hs38Dh.fa as the reference genome. In the absence of a known intervals list what should I do when performing Mutect2 variant calling? Should I use the wgs_calling_regions_hg38.interval_list?
Thank you very much.


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