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

RNAseq short variant discovery (SNPs + Indels) Follow


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    An Zheng

    Hi Team,


    Thanks for your incredible work. I'm looking for RNA-Seq somatic SNPs and indels calling pipeline and I found this article. However when I enter the github pages ( it shows "germline short variant discovery", not somatic. Do you have somatic short variant discovery pipeline? Thank you.



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    Brittany Goods

    Hi All, 

    I was wondering if this pipeline has been moved to Terra yet? I am a Terra user (still new) and would love to use this via Terra on a bunch of my data!! 




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    Owen Wilkins

    An Zheng curious if you found a solution to your question regarding somatic calls?

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    Matthieu J. Miossec

    The github link goes to an outdated version of the pipeline. :)

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