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 calling for plant



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    Pamela Bretscher

    HI Lina Herliana,

    I believe you should be able to run Mutect2 in multi-sample mode using your time point samples from the same plant and your PoN. In multi-sample mode, there doesn't need to be a matched-normal for each sample because all normals are pooled together. Here is a link to the Mutect2 FAQ and a previous forum post discussing the applications of Mutect2 multi-sample mode that you may find helpful. Please let me know if this does not answer your question. 

    Kind regards,


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    Lina Herliana

    Hi Pamela,

    Yes, it does answer my question.



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