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

MarkDuplicates analysis of large wheat chromosomes

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    Genevieve Brandt (she/her)

    Hi John,

    Could you share your entire command, stack trace, and GATK version? We did have a somewhat similar issue come up with the wheat genome and MarkDuplicates but I don't have enough information about your case to know if there is a good workaround.

    Best,

    Genevieve

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