We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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 for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
How do people chain Samtools and GATK mains together??
I am writing a Java program to a call a number of CommandLine classes in succession to sort, reorder, index I call SortSam, CleanSam,AddOrReplaceReadGroups, ReorderSam. Each call has a main which calls System.exit. Instead if calling that main (which would kill my pipeline, I call instanceMain on the relevant class using reflection. I want to pass as output file tmp.bam and expect tmp.bai to be generated as an index. That works. After I call invokeMain I want to rename the tmp file and the tmp index to the original names. I first rename the original to get it out of the way and also the original index file . My problem is that the original index file has not been closed and cannot be moved out of the way. While it is true that calling System.exit (as the CommandLine main does) addresses this issue - this is a VERY BLUNT HAMMER and precludes writing a program which chains command line operations. How can I close the index file without calling System.exit