Config file filters

[kw10]

Hello

I am running Mutect2 and wondering if the filters in the example configuration file are all optional? For example, if we do not want filtering based on AD, VAF, etc. can we set everything in the config file to "use in filter: false" and still run FIREVAT to filter out FFPE artefacts, OXO-G, etc.?

Thanks
Kim

[khb7840]

It's optional because the format of vcf is quite diverse. You can modify the config files as you want.

[kw10]

So if I use "filter: false" on all of the filters in the Mutect2 config file, will FIREVAT still perform filtering of FFPE and OXO-G artefacts? If not, can you tell me which filters are used to control the FFPE artefact and OXO-G artefact filtering?

Thanks

[khb7840]

If you set "use_in_filter" as false for all filters, it will not filter anything. From our analysis, major factors were base quality (BQ), allele fraction (VAF) and read count (AD). You may use just base quality for filtering.