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.
Installing GATK4 via Conda
Hi there! I have a small problem, or a suggestion for improvement, related to the use of (Mini)conda and GATK4. I'm not entirely sure if this forum is a right place to ask this because I don't really know how GATK4's Conda package is maintained, but let's give it a try!
So I'm using a wide variety of bioinformatic tools in my work which is why I prefer Conda in package management - just to make it little bit easier to handle package dependencies and package updates. I am now planning to try the new GATK4 as the version 126.96.36.199 seems to be available in Bioconda. With GATK3 I was able to launch GATK simply with command 'gatk' so I naturally tried the very same command for GATK4. However;
bash: gatk: command not found
bash: gatk4: command not found
I located the GATK4 .jar file and succesfully tried the command;
java -jar /home/user/miniconda3/pkgs/gatk4-188.8.131.52-py36/share/gatk4-184.108.40.206-0/gatk-package-4-0.0.1-local.jar -h
This prints all available tools as excepted. So the main problem seems to be that shortcut to this .jar file is not included in the Conda distribution. Is there any particular reason for this behaviour or is this just a bug in the package? It is, of course, possible to use GATK4 with 'java -jar' command but the use of simple 'gatk' or 'gatk4' would be easier for Conda users. For example, if I update my GATK4 in the future I must also update my pipelines so that my paths are leading to the right .jar file. If I use direct 'gatk4' command, in turn, I can simply update GATK4 with Conda and launch it with 'gatk4' command in my pipeline - without manual path updating.