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Further information about MuTect2 filters (clustered_events, homologous_mapping_event etc.)
Dear GATK developers,
We are using MuTect2 for variant calling and we have noticed that several variants fail to pass filters such as clustered_events, homologous_mapping_event, str_contraction and t_lod_fstar. We have reasons to believe that at least several of these variants could be incorrectly filtered out by MuTect2. For example, several variants that are positioned very closely to each other have been filtered out as clustered_events, although they have been previously verified and confirmed using Sanger sequencing.
I am aware that these filters are briefly described in the VCF file header (e.g. ##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">). However, I would like to ask whether there are any better definitions and further information about these filters and whether there are ways of manipulating or disabling them.
Thank you for your help.