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

Mutect2 somatic mutation identification stopped


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    Bhanu Gandham

    Hi Yuan Feng


    This could be a BAM indexing issue, and here are some suggestions to resolve that:
    1) can you please regenerate your bam index and try rerunning?
    2) If that doesn't work can you please retry with the latest GATK (

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