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.
MarkDuplicates error Value was put into PairInfoMap more than once
I get this error from a MarkDuplicates and all the questions I've found online comment on merging fastq file and ending up with read name from more than one original fastq files. I get this error without having merged fastq files and only having one pair of reads in bam file with same name with flags 129 and 81 (so read 2 and read 1). Is there any other reason why this message could come up?
I'm using an older version of the Picard (as a part of pipeline) though so if there has been bugs in this area then I'm likely hitting them.