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Strelka specifications

Information


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 https://codeload.github.com/Illumina/strelka/tar.gz/v2.8.3
Registration required No
Maintained Yes

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Maintainers


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

Publications for Strelka

Strelka in pipelines

 (7)
2017
PMCID: 5437943
PMID: 28327945
DOI: 10.1093/gigascience/gix015

[…] copy number estimates from genome and exome data. we implemented workflows that perform the required annotation and preprocessing of raw mutation and copy number outputs from tools such as strelka and sequenza, respectively. we ran these two workflows on 96 tumor/normal pairs representing dlbcl patients. the snv and indel calls were annotated and converted to mutation annotation format […]

2017
PMCID: 5477513
PMID: 28548104
DOI: 10.1038/ncomms15290

[…] x ten system. the sequence reads were aligned to the genome (hg19) using the bwa mem (v0.7.4) with default parameters. duplicates were removed using picard. the somatic mutations were called by strelka. final somatic calls were filtered to require a quality score of >30 and were further annotated by snpeff and snpsift. non-negative matrix factorization was applied to the 96-substitution […]

2017
PMCID: 5754767
PMID: 29203670
DOI: 10.1073/pnas.1708391114

[…] with hiseq2500 (illumina) were aligned to the mouse genome using gsnap (). for whole-exome sequencing, somatic single-nucleotide variants (snv) and insertion/deletions (indel) were called using strelka 1.0.4 (). protein altering mutations include nonsynonymous mutations, gain/loss of stop codon, insertion/deletion, and mutations at splicing donor and acceptor sites. criteria for recurrent […]

2016
PMCID: 4897744
PMID: 27265895
DOI: 10.1038/ncomms11790

[…] 500 (illumina). the reads were aligned to human reference genome hg19 using bwa 0.7.9a (ref. ) and pcr duplicate reads were filtered out using samblaster. somatic variant calling was performed using strelka. for 15 cases in the discovery cohort, mp-wgs libraries were prepared using the nextera mate pair library preparation kit (illumina). paired 2 × 76 bp reads were produced from the mate-pair […]

2015
PMCID: 4597064
PMID: 26424171
DOI: 10.1186/1471-2105-16-S13-S7

[…] and base quality recalibration. copy number data was computational inferred using exomecnv v1.4 []. single nucleotide variants (snvs) and small insertions and deletions (indels) were called using strelka v1.0.14 [] (tumor and normal pairs), resulting in variant call format (vcf) files. snpeff v4.0e [] was used to annotate each variant with its predicted functional effects., rna-seq samples […]


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Strelka in publications

 (138)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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