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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    Saeed Farajzadeh Valilou


    I am using the following command for each autosomes and sex chromosome intervals in HaplotypeCaller and I receive memory insufficient error. See the below for the error. Could anyone give a solution for this? FYI, I am using large cluster (great amount of RAM, CPU...) and data are recalibrated CRAM files of WGS. 

    gatk --java-options "-Xms20G -Xmx20G -XX:ParallelGCThreads=2" HaplotypeCaller \ 


    ERROR Message:


    # There is insufficient memory for the Java Runtime Environment to continue.

    # Native memory allocation (mmap) failed to map 21474836480 bytes for committing reserved memory.


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    Bo Xiao

    Dear GATK team,

    I'd like to ask a question about the parameter Settings of HaplotypeCaller. When doing SNP calling, I only want to refer to some scaffolds of the reference genome (like just autosomes), what parameters should be added? 

    Thanks and all the best,

    Bo Xiao

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