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.bam could not find the mutation, but bqsr found the mutation



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    Pamela Bretscher

    Hi cjz,

    Could you take a look at this troubleshooting document for when Mutect2 does not call an expected variant and see if any of the information and suggestions are useful in your situation?

    Kind regards,


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    Hi cjz,

    Please may I ask if you managed to resolve the issue described in your initial post above? If so, what was the cause, and please could you advise on how it was resolved?

    Thank you for your time and help.

    Kind regards.

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