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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

PMCID: 5940840
PMID: 29739933
DOI: 10.1038/s41467-018-04128-5

[…] 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 […]


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

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

[…] 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 […]


An integrated clinical and genomic information system for cancer precision medicine

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 […]


Identification of somatic mutations in monozygotic twins discordant for psychiatric disorders

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

[…] disorder in this table). after tas, the allele fractions of controls were found to be <0.316% (the assumed error rate). the genomic positions are based on the human reference genome (grch37), strelka and further filtering procedures yielded 22 hc candidates (supplementary tables ), five of which were validated by tas (supplementary tables ). hence, the validation rates for strelka […]


Somatic activating mutations in MAP2K1 cause melorheostosis

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

[…] 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 […]


Clinically actionable mutation profiles in patients with cancer identified by whole genome sequencing

PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] alignment tool, within basespace (illumina). somatic single nucleotide (snv) and insertion/deletion (indel) variant calling analysis was performed using the tumour-normal application v1.0, based on strelka, within basespace. calls were annotated using variantstudio v2 (illumina), a software using variant effect predictor (vep) v2.8, cosmic v77 and 1000 genomes (v3). in a second approach, data […]

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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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