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QuantiSNP specifications


Unique identifier OMICS_00730
Name QuantiSNP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Joannis Ragoussis

Publication for QuantiSNP


QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data

2007 Nucleic Acids Res
PMCID: 1874617
PMID: 17341461
DOI: 10.1093/nar/gkm076

QuantiSNP citations


A remark on copy number variation detection methods

PLoS One
PMCID: 5922522
PMID: 29702671
DOI: 10.1371/journal.pone.0196226

[…] Hapmap Project provided a CNV calling report based on SNP microarray data using QuantiSNP [] and Birdseye []. The 1000 Genome Project also provided a DNA structural variation report as a VCF file based on NSG data. Both reports were published with extra experimental information i […]


Genome wide detection of copy number variation in Chinese indigenous sheep using an ovine high density 600 K SNP array

Sci Rep
PMCID: 5430420
PMID: 28424525
DOI: 10.1038/s41598-017-00847-9

[…] is currently the most widely used for Illumina chips (PennCNV: 955 citations; QuantiSNP: 432 citations), particularly for high-density SNP data. Compared to other algorithms such as CNVPartition and QuantiSNP, PennCNV is more reliable for assessing the number of copies when using Illumina high-density arrays because it incorporates the allelic intensity ratio at each SNP marker and the total sign […]


High mutation rates explain low population genetic divergence at copy number variable loci in Homo sapiens

Sci Rep
PMCID: 5320550
PMID: 28225073
DOI: 10.1038/srep43178
call_split See protocol

[…] ep process according to Altshuler et al. The first step is to detect copy number variation on each chromosome by analyzing the probe-level intensity data from both the Affymetrix and Illumina arrays. QuantiSNP and Birdseye algorithms are used to identify CNV loci separately. Common CNV loci are further identified, and refined to ensure qualified copy number variant calls. The second step is to det […]


Copy Number Variants in Alzheimer’s Disease

PMCID: 5115612
PMID: 27662298
DOI: 10.3233/JAD-160469
call_split See protocol

[…] tect submicroscopic CNVs that are not recognized by the routine karyotype analyses.There are several algorithms and tools available for inferring CNVs from SNP data []. The most known are PennCNV [], QuantiSNP [], iPattern [], and some proprietary software (e.g., CNVpartition, implemented in Illumina BeadStudio, and Affymetrix Genotyping Console). PennCNV is an algorithm based on Hidden Markov Mod […]


Genome wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high density 600K SNP arrays

Sci Rep
PMCID: 4901276
PMID: 27282145
DOI: 10.1038/srep27822

[…] logy, CNV detection using SNP chip data has been conducted in humans and animals. Several algorithms for inferring CNV based on SNP chip data have been developed, including PennCNV, cnvPartition, and QuantiSNP. No single approach can capture all CNV; thus, one may be complementary to another. However, most studies on CNV using SNP arrays in animals and humans have used only PennCNV software, espec […]


CNTN6 mutations are risk factors for abnormal auditory sensory perception in autism spectrum disorders

Mol Psychiatry
PMCID: 5378808
PMID: 27166760
DOI: 10.1038/mp.2016.61

[…] detection, 1534 unrelated individuals with ASD (901 from Pinto et al. and 633 from our cohort) and 8936 controls were analyzed using Illumina SNP arrays (). Two CNV detection algorithms, PennCNV and QuantiSNP, were used and all samples met stringent quality control criteria as described. For SNV detection, 429 individuals (212 independent patients with ASD and 217 controls) were screened for muta […]


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QuantiSNP institution(s)
Genomics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, UK

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