Strelka

Overview

Strelka (and its successor Strelka2) is a somatic small-variant caller for matched tumor-normal whole-genome or whole-exome sequencing data. It uses a Bayesian statistical model to call single-nucleotide variants (SNVs) and small insertions/deletions (indels), explicitly accounting for sequencing error rates, local depth variation, and tumor purity. Strelka2 added support for germline variant calling and improved sensitivity for indels in homopolymer regions.

Used by

  • Used to call somatic SNVs and indels from paired tumor/normal WGS data (hg19 BWA alignment) for 28 metastatic neuroendocrine neoplasms in the BC Cancer Personalized OncoGenomics (POG) program; results fed into TMB estimation (median 2.19 mut/Mb), mutational signature analysis, and actionability assessment PMID:24326773.
  • Used for somatic variant calling in whole-genome sequencing of four CRC primary/metastasis trios to validate MSK-IMPACT findings. PMID:25164765
  • Used for somatic variant calling in MPNST WES discovery cohort (15 tumors) PMID:25240281
  • Strelka used for somatic SNV calling in whole-exome sequencing of adrenocortical carcinoma PMID:26095796
  • Used for SNV calling in whole-genome sequencing of 46 matched primary/recurrent medulloblastoma samples alongside MutationSeq; contributed to characterization of massive genetic divergence (mean <12% shared events) between primary and recurrent tumor clones PMID:26760213.
  • Used alongside Indelocator for indel calling in 619 CRC FFPE tumor/normal WES pairs; only calls concordant between both tools were retained PMID:27149842
  • Used Strelka for somatic indel and SNV calling in paired tumor-normal samples PMID:28373299
  • Applied alongside MuTect, SomaticSniper, and VarScan for somatic variant calling in 68 paired melanoma WES samples; intersection-based approach used to increase specificity PMID:29033130
  • Strelka used for somatic variant calling in 35 metastatic CCRCC paired tumor/normal WES samples alongside MuTect for the PBRM1-immunotherapy response study PMID:29301960
  • Used to call indels (v1.0.11) across 1,013 prostate tumor/normal pairs in the prad_p1000 dataset PMID:29610475

Notes

  • Designed for paired tumor-normal analysis; lower sensitivity in tumor-only or low-purity samples than in high-purity matched pairs.
  • Strelka (v1) and Strelka2 (v2) have different calling models; downstream comparisons should specify version.
  • Commonly used alongside structural-variant callers (ABySS, Manta) in comprehensive WGS pipelines.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:25164765

This page was processed by crosslinker on 2026-05-14. - PMID:25240281

This page was processed by crosslinker on 2026-05-14. - PMID:26095796

This page was processed by crosslinker on 2026-05-14. - PMID:26760213

This page was processed by wiki-cli on 2026-05-14. - PMID:27149842

This page was processed by wiki-cli on 2026-05-14. - PMID:28373299

This page was processed by wiki-cli on 2026-05-14. - PMID:29033130

This page was processed by entity-page-writer on 2026-05-15. - PMID:29301960

This page was processed by wiki-cli on 2026-05-15. - PMID:29610475

This page was processed by wiki-cli on 2026-05-15.