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.
Is there a panel-of-cancer option for somatic variant calling
I am trying to identify somatic variants from 18 pairs of matched tumour/normal samples from a single cancer type.
I've done the tutorial at https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2. The idea of panel-of-normals makes a lot of sense to me. So I am wondering if there is an option to call somatic variants of all tumour samples concurrently (hence panel of cancer) w.s.t. the panel of normals, leveraging information from all tumour samples together somehow with GATK4 mutect2?