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

HS_PENALTY_20X is -1 on one version of GATK, crashes on newest version.


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    Bhanu Gandham

    HI JonR


    I believe you are facing this issue because you are using `interval.list` instead of `interval_list` suffix. Can you please change that and retry to see if it resolves the issue? This is a known issue.

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