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

GATK4.1.7.0 specific error: "htsjdk.samtools.SAMException: Cannot read non-existent file:"

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    Tiffany Miller

    Interesting. Can you try renaming "interval.list" to "interval_list"  to see if that works? I wonder if you are encountering this issue

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    JonR

    That worked.  Thank you Tiffany Miller!

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