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

Multi sample somatic calling Mutect2



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    Gökalp Çelik

    Hi avrajit

    We don't have any multi-sample somatic calling workflow for Mutect2 and we don't have a means to combine individual VCFs produced by Mutect2 for routine use due to tags and VCF structure being different than otherwise germline VCF files. However you may use other existing tools out there to combine your files but your mileage may vary. 


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    Hi Gokalp

    Thanks for your response. 

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