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.
Using GATK as a library
We are using GATK as part of our internal pipelines written in Java. Currently we are making command-line calls to the GenomeAnalysisTk jar, but this generated intermediate files and it would be better if we could just directly call the relevant functions in the target and hold the results in memory. Reading the source it is not immediately obvious so I was hoping for some guidance. As an example of a how we use it as part of our pipeline:
java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R -I -o
java -jar GenomeAnalysisTK.jar -T IndelRealigner -R -targetIntervals -I --o <realigned.ban>