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99.76% of reads failing DuplicateReadFilter for targetome analysis

nitinCelmatixnitinCelmatix NYCMember
edited February 2016 in Ask the GATK team

Hi,
I am using GATK HC to identify variants in a target region of about 23kb with very deep sequencing. I get this message during HC that 99.76% of reads failing DuplicateReadFilter. This means that a lot of my reads are being thrown out and hence I am not getting correct variant calls.

First, is GATK HC an appropriate tool to call variants in such a small region with deep sequencing (more than 100X)?
Second, how can I rectify this error of 99% reads failing DuplicateReadFilter?

Thanks,
Nitin

Best Answer

Answers

  • Thanks Shlee, this helps a lot.
    Also, is HC the only step where I should use this option "-drf DuplicateRead" or should I use in in any other step in the pipeline as well?

    Thanks!

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    I would recommend using this option in all steps downstream of duplicate marking.

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