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 Mismatch between the reference haplotype and the reference assembly graph path.


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    Genevieve Brandt (she/her)

    Hi Heejun Jang,

    Could you try updating your GATK version since we have done some bug fixing with Mutect2 since We are currently on and so far it has been a great release without many issues!



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