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

Some MarkDuplicates chunks take a very long time to run


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    Tiffany Miller

    Hi there! The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    That being said, I'll offer a quick few thoughts though it doesn't answer your main question. Have you tried MarkDuplicatesSpark to increase speed? It will typically run faster than MarkDuplicates and SortSam by a factor of 15% over the same data at 2 cores and will scale linearly to upwards of 16 cores.

    This thread offers thoughts on settings.

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