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Adding read filters to HC

simono101simono101 London, UKMember

Dear GATK Team,
If I specify a read filter using the -rf option, is that read filter added to the filters applied by default, or will that then be the only filter that is applied (so I would also need to specify the defaults to ensure they were all run.

e.g. I want to add a bad cigar filter...

-rf BadCigar

But I also want the default filters applied, namely:

  • NotPrimaryAlignmentFilter
  • FailsVendorQualityCheckFilter
  • DuplicateReadFilter
  • UnmappedReadFilter
  • MappingQualityUnavailableFilter
  • HCMappingQualityFilter
  • MalformedReadFilter

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