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Not surprisingly, GATK is available through conda. After some trial and error it seems there are 2 extras needed to get it up and running. 1. conda-forge, and 2. needing to specify that we want the most recent version (this is similar to what you see with spades). I would suggest giving it its own environment perhaps "GVA-gatk"
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conda create --name GVA-gatk -c bioconda gatk4 conda activate GVA-gatk gatk --version conda-forge -c bioconda gatk4=4.4.0 conda activate GVA-gatk gatk --version |
The first thing you will see is a comment about javvva and the "jar being used. If you are on the headnode, i expect you will get an error message about memory related to java, otherwise your output should be:
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The Genome Analysis Toolkit (GATK) v4.24.60.10 HTSJDK Version: 23.240.15 Picard Version: 23.270.10 |
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gatk --list |
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Rather than using sample data specifically for this tutorial, we will instead do a small tutorial based on our read mapping tutorial and samtools SNV tutorial from day 2 of the course. Assuming you completed that tutorial you the following tutorial should work.
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As mentioned this is a very small introduction to GATK adapted from one of the broad's tutorials which can be found here. There are numerous other tutorial links for on the GATK website you can begin to work with now that you have verified your installation and begun troubleshooting some of the quirks of the program.
Return to GVA2022 GVA2023 home page.