Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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    Field -Ye Tian

    Dear GATK team,

    I'd like to thank you for your dedication and efforts to push forward the bioinformatics. 

    I'm not a professional bioinfomatic person. I've been exploring with the GATK best practice pipeline with my WES data. 

    I got stuck at MarkDuplicatesSpark, which requires a JDK8 to run but I have JDK11 installed.

    I got the exact same error message. 

    I had a conda environment established and installed a JDK8 there. However, I have to run a ./java -version under the installed folder to see a JDK 1.8. Otherwise, when I type java -version anywhere else, I see version 11. 

    I wonder under this circumstance how am I supposed to run MarkDuplicatesSpark. I hope that I can add an java option somewhere within the command but not sure. 

    Hopefully you could also add the solution to the MarkDuplicatesSpark manual as newer versions of java will be gaining popularity. 


    All the best and thank you.


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