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

gatk stack memory insufficient to run Mutect2 for artifact correction

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    Genevieve Brandt (she/her)

    Hi Uma Saxena

    Thanks for writing into the forum about this issue! This actually doesn't look like a memory issue, this message indicates an issue with Mutect2 or the data:

    java.lang.IndexOutOfBoundsException: Index: 0, Size: 0

    Could you send in a snippet of your bam file that recreates this issue to our bug reporting ftp site following these instructions? We'll try to get to the bottom of what is going on. Let me know when you have done this and the name of the file.

    Best,

    Genevieve

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