Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

Read Filter "Duplicates"

MaxMax Member
edited April 2014 in Ask the GATK team

Hi !

I just looked through the automatically applied Read Filters of the DepthOfCoverage Walker and saw that both, the NotPrimaryAlignmentFilter as well as the DuplicateReadFilter, are applied. However, according to the Docu, both should simply remove the marked PCR Duplicates.
I also realised that the MappingQualityUnavailableFilter and the MappingQualityZeroFilter seem to do the same things, too. (According to the documentation both filter out mapping quality zero reads. ).

Therefore I wondered, if there is a reason for these read filter "duplicates"; so is there any difference between the mentioned filters ?

Thanks for your help !

Tagged:

Best Answers

Answers

  • MaxMax Member

    Hi Geraldine,

    thanks for your prompt answer !
    So then I would assume, the DuplicateReadFilter to remove the marked PCR Dups, the MappingQualityZeroFilter to remove Reads with MQ==0, the MappingQualityUnavailableFilter to remove Reads with a MQ that is not available and the NotPrimaryAlignmentFilter to remove reads that do not map uniquely (only the best (primary) one remains)

    Is that correct ?

Sign In or Register to comment.