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Strelka
Strelka2 is 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 uses a tiered haplotype model to improve accuracy and provide read-backed phasing. The caller adaptively selects 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.
Somatic calling 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 rescoring step using random forest models trained on various call quality features has been added to both callers to improve precision.
For more information, visit github.com/Illumina/strelka.
For Research Use Only. Not for use in diagnostic procedures.