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.
Proper regex to mark duplicates using Picard tools on SOLiD data
I'm having trouble removing duplicates using Picard tools on SOLiD data. I get a regex not matching error.
The reads have the following names:
And I don't think Picard tools is able to pick these read names with its default regex.
I tried to change the default regex. This time it does not throw an error, but it takes too long and times out (out of memory). I suspect I'm not giving the right regex. Here is my command:
java -jar $PICARD_TOOLS_HOME/MarkDuplicates.jar I=$FILE O=$BAMs/MarkDuplicates/$SAMPLE.MD.bam M=$BAMs/MarkDuplicates/$SAMPLE.metrics READ_NAME_REGEX="([0-9]+)([0-9]+)([0-9]+).*"
Any help is appreciated. Thanks!