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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.
High depth - tumor-only variant calling with mutect2
I'm trying to call somatic variants (snv and indels) on targeted sequencings (usually from amplicon-based enrichment). Using Mutect1 seems to work very well, but MuTect2 is proving more difficult with reported frequencies often over-evaluated compared to IGV, high false positive and false negative rates.
I have seen threads about some parameters for deep(er) sequencings or tumor-only calling or amplicon panels, but I'm wondering if there is a set of "best-practices" and parameter values that could be beneficial in this particular setting.
The sequencing depths span from ~500 to 10-20000 reads and the breadth of sequencing ranges 10 to 100 Kb. In amplicon data, some positions in each amplicon are covered only by one read-orientation (extremities of amplicons) and others by both, with a short transition. There are no normal samples.
(currently, I'm using mutect2 on gatk3 but information on gatk4 would of course be welcome too)
Thanks and good day,