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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,


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Boris,

    Which version of GATK are you using? Can you test this on just one site where the duplicate read filter should definitely come into play? For example, you can just run on a single base which has duplicate reads covering it. Can you post the BAM file and output record for that site?

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