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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,