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

SPLICE_SITE specification in Funcotator



  • Official comment
    Jonn Smith

    Hi Zhan,

    The default is 2 bases.  It looks like this argument was never exposed to the user, so currently there is no way to configure it at runtime (this is a bug!).  

    I'll add an issue in the GATK github.  It should be a relatively quick update.



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    yinxiu Zhan

    Hi Jonn,

    thanks a lot for the clarification



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