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Changing or Removing Filters

Hi,
I would like to know how to see what filtering is applied to the variants, their default values, and how I might be able to change them. I have read the filters mentioned in the paper but I would like to maybe remove/change some of the filters.

Right know you only have "REJECT" as the comment if a variant is filtered, is there another way to tell why a variant is filtered?

Thanks for you help!
Shawn

Answers

  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    The easiest way to get some insight in to which filter are being triggered and why is to run with the

    --enable_extended_output

    option. This will output many more columns of information including the values for all the filters as described in the publication. In addition, there will also be a column "failure_reasons" that will tell you exactly what filter(s) caused the mutation to be rejected.

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