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

GatherBQSRReports OSError: [Errno 2] No such file or directory, but does not show which is missing


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    Gökalp Çelik

    Hi JooYoung Park

    This error message is not specific to GATK related tool but the installation of GATK itself. Looks like gatk python script is unable to find the proper jar files in the path to start the run. Can you check your GATK installation folder?

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