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GATK 3.5 FindCoveredIntervals works same regardless of DuplicateFilter tag
When using FindCoveredIntervals tool, I find no difference when calling the tool with -drf DuplicateRead tag, or without it (when using -rf DuplicateRead tag).
Manual checking of .bam file using IGV shows that duplicate reads are existing in the input .bam, and that resulting .bed files ignore intervals where duplicate reads increase coverage over given threshold in both cases (with or without a flag).
Is this bug already known, I haven't been able to find similar questions on the forum? Is it fixed in later versions of GATK, and is there (or will there be) same or similar tool in GATK 4.0? Am I using DuplicateRead filter wrong and expecting wrong result?
Thanks in advance,