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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

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Known Issues with Mutect2 GATK4.1 Follow

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GATK Team
  • Updated
  • Error:
    java.lang.IllegalArgumentException: log10p: Log10-probability must be 0 or less when running FilterMutectCalls(GATK4.1) to Filter VCF results called by Mutect2.
    Solution:
    This error is fixed in master as of March 19th 2019. It will be released in the GATK version 4.1.1.0.

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    elcortegano

    I'm getting this error on GATK4-4.2.1.0-0.

    It only seems to appear enabling `--mitochondria-mode true`, but I need this option.

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