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

java.io.IOException: Input/output error

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    Gökalp Çelik

    Hi yujie yan

    Given the fact that a smaller reference genome works but a larger one does not tells me that there is an IO bottleneck/issue/permission problem etc. present that prevents GATK to reach that resource properly. Can you localize your files to the server directly if those files are only present on an NFS/SMB partition and see if that works?

     

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