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

Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller

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    Anthony Dias-Ciarla

    Hi Blaz Vrhovsek,

    Thank you for writing to the GATK Community Forum. We hope that we can adequately address your question.

    We would suggest that you try setting the following two environment variables to and then re-running the tool.

    export MKL_NUM_THREADS=1
    export OMP_NUM_THREADS=1

    Let me know if that works.

    Best,

    Anthony

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