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Further information about MuTect2 filters (clustered_events, homologous_mapping_event etc.)

alex_mizealex_mize Prague, Czech RepublicMember

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.

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @alex_mize
    Hi,

    Currently, we are working on documenting the MuTect2 annotations, but we don't have anything public yet. Also, you cannot manipulate the filters yet, but have a look at this thread.

    We now have a team focused on improving MuTect2, so you can expect some really great changes/updates in the next few months :smile:

    -Sheila

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