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Difference between DuplicateReadFilter and NotPrimaryAlignmentFilter?

tommycarstensentommycarstensen United KingdomMember ✭✭✭
edited March 2015 in Ask the GATK team

I have a quick question. What is the difference between DuplicateReadFilter and NotPrimaryAlignmentFilter? The documentation for each of them is identical; i.e.

Filter out duplicate reads.

Best Answer

  • pdexheimerpdexheimer ✭✭✭✭
    Accepted Answer

    They look at different flags in the BAM file. DuplicateReadFilter checks the flag that is set by MarkDuplicates (0x0400), and NotPrimaryAlignmentFilter checks a flag that is set by the aligner (0x0100).

    The documentation for NotPrimaryAlignmentFilter should be corrected - it's actually removing any secondary alignments that the aligner reports (either multi-mapped reads or, e.g., reads split up by 'bwa mem -M')

Answers

  • pdexheimerpdexheimer Member ✭✭✭✭
    Accepted Answer

    They look at different flags in the BAM file. DuplicateReadFilter checks the flag that is set by MarkDuplicates (0x0400), and NotPrimaryAlignmentFilter checks a flag that is set by the aligner (0x0100).

    The documentation for NotPrimaryAlignmentFilter should be corrected - it's actually removing any secondary alignments that the aligner reports (either multi-mapped reads or, e.g., reads split up by 'bwa mem -M')

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭
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