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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

Mutect2 failing to produce F1R2.tar.gz files on TCGA bam (tumor-normal pairs)

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    Genevieve Brandt (she/her)

    Hi TMB, could you share the entire stack trace

    Thank you!

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    TMB

    Hi Genevieve, 

    Thank you for your response. I did notice there is an GC error  as follows:

    Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

    I used "-Xmx75G" instead of "-Xmx6G" and it worked fine. 

    TMB 

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    Genevieve Brandt (she/her)

    Thanks for the update, TMB, glad you were able to solve the issue! One note: you might not need 75G of memory, 16G might be enough.

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    황신원

    Hi, I have a same error about memory problem. 

    My data is whole genome sequencing 30X~60X data and I use 16GB memory but error occurred. Is there any proper memory recommendation for whole genome sequencing data?

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    Genevieve Brandt (she/her)

    Hello,

    To help with runtime or memory usage, try the following:

    1. Verify this issue persists with the latest version of GATK.

    2. Specify a --tmp-dir that has room for all necessary temporary files.

    3. Specify java memory usage using java option -Xmx.

    4. Run the gatk command with the gatk wrapper script command line.

    5. Check the depth of coverage of your sample at the area of interest.

    6. Check memory/disk space availability on your end.

    Hope this helps!

    Genevieve

     

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