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.
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.


mohamadzamanimohamadzamani Member
edited April 9 in Ask the GATK team
What is meaning of error "INVALID_MATE_REF_INDEX" in a SAM/BAM file and How fix it?
Post edited by mohamadzamani on

Best Answer


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
  • mohamadzamanimohamadzamani Member
    I previously saw above link in detail. In this page, only possible problems were listed and no details or solution provided for them. This is a clear weak point for GATK, which cant properly guide users.
  • mohamadzamanimohamadzamani Member
    Dear bhanuGandham
    Many thanks indeed for your reply.
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