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Strelka2

  • Description

    a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. The germline caller employs an efficient tiered haplotype model to improve accuracy and provide read-backed phasing, adaptively selecting between assembly and a faster alignment-based haplotyping approach at each variant locus. The germline caller also analyzes input sequencing data using a mixture-model indel error estimation method to improve robustness to indel noise. The somatic calling model improves on the original Strelka method for liquid and late-stage tumor analysis by accounting for possible tumor cell contamination in the normal sample. A final empirical variant re-scoring step using random forest models trained on various call quality features has been added to both callers to further improve precision.

  • Usage

    To list all executables provided by Strelka2, run: $ biogrids-list strelka2 Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install strelka2 Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    S. Kim, K. Scheffler, A. L. Halpern, M. A. Bekritsky, E. Noh, M. Källberg, X. Chen, Y. Kim, D. Beyter, P. Krusche, and C. T. Saunders. 2018. Strelka2: fast and accurate calling of germline and somatic variants. Nature Methods. 15(8): 591-594.


    • *Full citation information available through

  • Keywords

    Genomics, Variant Analysis

  • Default Versions

    Linux 64:  2.9.2 (108.1 MB)
    OS X INTEL:  2.9.2 (63.0 MB)

  • Other Versions

      Linux 64:

    • OS X INTEL:

      2.9.9 (63.3 MB)

  • Developers

    Christopher T Saunders, Sangtae Kim

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