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