Strelka protocols

Strelka specifications

Information


Unique identifier OMICS_00093
Name Strelka
Alternative name Strelka2
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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Documentation


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

 (3)
2017
PMCID: 5754767
PMID: 29203670
DOI: 10.1073/pnas.1708391114

[…] with hiseq2500 (illumina) were aligned to the mouse genome using gsnap (34). for whole-exome sequencing, somatic single-nucleotide variants (snv) and insertion/deletions (indel) were called using strelka 1.0.4 (35). protein altering mutations include nonsynonymous mutations, gain/loss of stop codon, insertion/deletion, and mutations at splicing donor and acceptor sites. criteria for recurrent […]

2014
PMCID: 4231324
PMID: 25394353
DOI: 10.1038/srep07063

[…] dna exome sequencing data from tcga5 (supplementary table s1). there were 149,959 single-nucleotide variants (snvs) and 10,000 insertion/deletions (indels) detected using the variant caller, strelka6 (see supplementary material section i for results from an alternative variant caller and reasons for our selection of strelka). protein coding mutations were annotated by annovar8 […]

2014
PMCID: 4231324
PMID: 25394353
DOI: 10.1038/srep07063

[…] 10,000 insertion/deletions (indels) detected using the variant caller, strelka6 (see supplementary material section i for results from an alternative variant caller and reasons for our selection of strelka). protein coding mutations were annotated by annovar8 and splicing mutations with the shannon human splicing pipeline18 (table 1, see supplementary tables s2–4 for a list of all mutations). […]

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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