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QuantiSNP specifications

Information


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

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Maintainer


  • person_outline Joannis Ragoussis <>

Publication for QuantiSNP

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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 in pipeline

2010
PMCID: 2898065
PMID: 20482838
DOI: 10.1186/gb-2010-11-5-r52

[…] santa clara, california, usa), birdsuite [] and ipattern (j zhang et al., manuscript submitted) were used to call cnvs. for illumina 1 m, the snp calling was done using the beadstudio software. quantisnp [] and ipattern were used to identify cnvs. for both platforms, only variants confirmed by at least two calling algorithms were included in the final set of calls., the agilent custom human […]


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QuantiSNP in publications

 (108)
PMCID: 5922522
PMID: 29702671
DOI: 10.1371/journal.pone.0196226

[…] would be returned in the same way where the splice junctions would be identified between exons in rna-seq analysis., 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 […]

PMCID: 5789005
PMID: 29379041
DOI: 10.1038/s41598-018-19520-w

[…] was claimed under a significance threshold of p-value < 0.05., furthermore, the intensity data of 497,849 snps were used to call the cnv regions. cnvs were identified using penncnv and quantisnp, respectively, which identifies cnvs by integrating intensity data from neighboring probes using a hidden markov model (hmm). gene-based cnvs association analysis was used to test whether […]

PMCID: 5580201
PMID: 28825658
DOI: 10.3390/s17081920

[…] hormone receptor (fshr) and the luteinizing hormone/choriogonadotropin receptor (lhcgr), with 61 and 19 snps respectively., we performed cnvs prediction in our dataset using the penncnv and quantisnp algorithms [,]. penncnv was executed using the -test option using default values. quantisnp algorithm was executed enabling the options-isaffy and -levels, since we used an affymetrix […]

PMCID: 5402652
PMID: 28438122
DOI: 10.1186/s12864-017-3658-x

[…] populations by powerfully detecting common and rare variants across the 5 most commonly studied subpopulations including african, admixed american, east asian, european, and south asian. using the quantisnp algorithm, 11 and 16 high confidence cnvs (max log bf > 10) were called in two replicates. of these 4 and 5 cnvs respectively met the 50% reciprocal overlapping criteria with a gold […]

PMCID: 5399367
PMID: 28429786
DOI: 10.1038/srep46490

[…] of all samples by three standard variation, or with median signal intensity deviating from median signal intensity of all samples by 1.5 interquartile range (iqr) were excluded., penncnv and quantisnp were used for cnv detection with genotype data of illumina microarray chips (omni one for gwas sub-population 1, omni zhonghua for gwas sub-population 3, and 610-quad for gwas […]


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

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