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qSNP specifications

Information


Unique identifier OMICS_00089
Name qSNP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A pair of tumor and normal files that have been duplicate-marked and coordinate sorted.
Input format BAM
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline John V. Pearson <>
  • person_outline Sean Grimmond <>

Publication for qSNP

qSNP citations

 (8)
library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] variants using the tumor and distinguish somatic variants from germline and loss of heterozygosity (loh) variants using the matched normal sample., the heuristic approaches, adopted by varscan2, qsnp, shimmer, radia, soapsnv, and vardict , , , , , , identify potential variants whose supporting reads meet certain thresholds and then apply statistical tests or ad hoc rules to isolate somatic […]

library_books

Germline and somatic variant identification using BGISEQ 500 and HiSeq X Ten whole genome sequencing

2018
PMCID: 5761881
PMID: 29320538
DOI: 10.1371/journal.pone.0190264

[…] (version 1.129, http://picard.sourceforge.net) and coordinates sorted using samtools (version 1.3) []. single nucleotide substitution variants (snv) were detected using a dual calling strategy using qsnp [] and gatk haplotypecaller []. short insertion and deletions (indels) of ≤50bp, were also called with the gatk haplotype caller. variants were annotated with ensembl v75 gene feature […]

library_books

Whole exome sequencing of an asbestos induced wild type murine model of malignant mesothelioma

2017
PMCID: 5455120
PMID: 28577549
DOI: 10.1186/s12885-017-3382-6

[…] 1.141, http://broadinstitute.github.io/picard/) and coordinates sorted using samtools (version 1.3) []. single nucleotide substitution variants were detected using a dual calling strategy using qsnp [] and the haplotype caller module of gatk []. short indels of ≤50 bp, were called with the haplotype. initial read quality filtering for all variants detected included: a minimum of 35 bases […]

library_books

Mitochondrial mutations and metabolic adaptation in pancreatic cancer

2017
PMCID: 5282905
PMID: 28163917
DOI: 10.1186/s40170-017-0164-1

[…] identified from exome-capture sequencing using solid v4 from primary tumours as previously reported [], or from patient derived xenografts and cell lines, sequenced using illumina hiseq 2000, using qsnp [] and pindel [], respectively, as described in []., for the identification of nuclear encoded mitochondrial genes that are mutated in pancreatic cancer, the published list of 1034 genes [], […]

library_books

A comprehensive assessment of somatic mutation detection in cancer using whole genome sequencing

2015
PMCID: 4682041
PMID: 26647970
DOI: 10.1038/ncomms10001

[…] well-performing ssm submissions with high values for both precision and recall. those with the highest f1 scores () were mb.q and mb.j, pipelines that combine two different somatic mutation callers: qsnp with gatk and sga with freebayes (). submissions with a high number of calls did not necessarily achieve higher recall; about two-thirds of all mutations (or >80% of tier 1 mutations) […]

library_books

Using the MCF10A/MCF10CA1a Breast Cancer Progression Cell Line Model to Investigate the Effect of Active, Mutant Forms of EGFR in Breast Cancer Development and Treatment Using Gefitinib

2015
PMCID: 4430383
PMID: 25969993
DOI: 10.1371/journal.pone.0125232

[…] and sequencing were performed following the manufacturer’s recommendations., sequencing data was aligned to the human genome (hg19) using bwa []. cell line specific variants were identified using qsnp [] (heuristic driven somatic/germline caller) and the genome analysis tool kit (gatk) [] (a bayesian caller). only variants that were called by both qsnp and gatk were used in subsequent […]


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qSNP institution(s)
Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; The Kinghorn Cancer Centre, and the Cancer Research Program, Garvan Institute of Medical Research, Sydney, NSW, Australia; Department of Surgery, Bankstown Hospital, Sydney, NSW, Australia; South Western Sydney Clinical School, University of New South Wales, Liverpool, NSW, Australia; University of Sydney, Sydney, NSW, Australia

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