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qSNP specifications


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




No version available


  • person_outline John V. Pearson
  • person_outline Sean Grimmond

Publication for qSNP

qSNP citations


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

Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] ential 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 va […]


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

PLoS One
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 information […]


Mitochondrial mutations and metabolic adaptation in pancreatic cancer

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

[…] e 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 [], was su […]


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

PLoS One
PMCID: 4430383
PMID: 25969993
DOI: 10.1371/journal.pone.0125232
call_split See protocol

[…] 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 analyses […]


Recommendations for Accurate Resolution of Gene and Isoform Allele Specific Expression in RNA Seq Data

PLoS One
PMCID: 4428808
PMID: 25965996
DOI: 10.1371/journal.pone.0126911

[…] both the aln, sampe (for the mate-pair data) and samse (for the fragment data) commands. Alignment files were transformed into BAM files and indexed using SAMTools v0.1.17 []. SNPs were called using qSNP v1.0 [] with the following approach: WGS aligned reads were filtered for PCR duplicates, and only those with an alignment length greater than 34bp (CIGAR M> = 34), an MD mismatch tag < = 4, and a […]


Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Nat Commun
PMCID: 4596003
PMID: 25351503
DOI: 10.1038/ncomms6224

[…] f 73% and deep WGS was performed at an average base pair depth of 74-fold for tumour and 39-fold for normal samples (). Somatic substitutions were identified using a dual-tool strategy using GATK and qSNP, while indels were identified using Pindel. Re-sequencing of one tumour/normal pair confirmed the accuracy of substitution calls to be 98.8%. Indels in coding regions were independently verified […]


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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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