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Strelka specifications


Unique identifier OMICS_00093
Name Strelka
Alternative names Strelka2, Strekla
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BAM
Output format VCF, BAM
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.9.6
Stability Stable
Source code URL
Registration required No
Maintained Yes




No version available



  • person_outline Christopher Saunders
  • person_outline Sangtae Kim
  • person_outline Konrad Scheffler
  • person_outline Aaron Halpern
  • person_outline Mitchell Bekritsky

Publications for Strelka

Strelka citations


Recurrent hotspot mutations in HRAS Q61 and PI3K AKT pathway genes as drivers of breast adenomyoepitheliomas

Nat Commun
PMCID: 5940840
PMID: 29739933
DOI: 10.1038/s41467-018-04128-5
call_split See protocol

[…] ibration were performed using the Genome Analysis Toolkit (GATK). Somatic single nucleotide variants (SNVs) were identified using MuTect; small insertions and deletions (indels) were identified using Strelka and VarScan 2,, and further curated by manual inspection. Variants found with >5% global minor allele frequency in dbSNP (Build 137) or that were covered by <10 reads in the tumor or <5 reads […]


Whole exome sequencing of cell free DNA and circulating tumor cells in multiple myeloma

Nat Commun
PMCID: 5923255
PMID: 29703982
DOI: 10.1038/s41467-018-04001-5

[…] eads around mutated sites with Novoalign to hg19 including decoy sequences and re-ran MuTect to filter out mutations in problematic regions. To call somatic insertions and deletions (indels), we used Strelka and annotated the mutation consequences using Oncotator. We also filtered out SSNVs and indels present in a panel of normal samples in order to filter out potential germline sites or recurrent […]


An integrated clinical and genomic information system for cancer precision medicine

BMC Med Genomics
PMCID: 5918454
PMID: 29697362
DOI: 10.1186/s12920-018-0347-9

[…] transcriptome sequencing (WTS, a.k.a. RNA-seq) data. We calculate the somatic single nucleotide variants (SNVs), insertions and deletions (INDELs), and copy number variations (CNVs) using Mutect [], Strelka [], and EXCAVATOR [], respectively. The MapSplice-RSEM [, ] pipeline was used for RNA-seq quantification to warrant accuracy in spite of long computation time. Galaxy [] pipelines for WES and […]


Identification of somatic mutations in monozygotic twins discordant for psychiatric disorders

NPJ Schizophr
PMCID: 5899160
PMID: 29654278
DOI: 10.1038/s41537-018-0049-5

[…] d candidates that were identical to candidates identified in the control samples, assuming that such sites were the result of sequencing errors and should be classified as false positives (MuTect and Strelka tolerate one or two base-calls of candidate mutations in control samples at default parameters, regarding those as sequence artifacts). Strelka computes an original score called Quality Score […]


Somatic activating mutations in MAP2K1 cause melorheostosis

Nat Commun
PMCID: 5895796
PMID: 29643386
DOI: 10.1038/s41467-018-03720-z

[…] nment around indels, and recalibrate base quality scores. The resulting BAM files (one per sample) served as inputs to somatic mutation callers (Fig. ).Two somatic mutation callers (muTect v1.1.7 and Strelka v1.0.14) were used, with default parameters for WES data. Somatic variants called by either method were annotated with functional impact and population frequency using ANNOVAR. We filtered som […]


Xome Blender: A novel cancer genome simulator

PLoS One
PMCID: 5886411
PMID: 29621252
DOI: 10.1371/journal.pone.0194472

[…] ing SNV, it calls SNV genotypes independently and its likelihood function assumes no Allelic specific expression (ASE). When read counts are very low, SAMtools/BcfTools may not call SNV genotypes []. Strelka takes as input the sequencing data files of tumor and normal samples in BAM format and by applying a Bayesian probability model define the most likely genotype. Variant detection is also based […]


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Strelka institution(s)
Illumina, Inc., San Diego, CA, USA; Illumina Cambridge Ltd, Essex, UK; Department of Computer Science and Engineering, University of California, San Diego, CA, USA

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