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CNVphaser specifications


Unique identifier OMICS_30288
Name CNVphaser
Alternative name CNVphaserPro
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes




No version available


  • person_outline Tatsuhiko Tsunoda

Publication for CNVphaser

CNVphaser citations


Hardy Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy number variations

Sci Rep
PMCID: 4357990
PMID: 25765626
DOI: 10.1038/srep09066

[…] in the virtually infinite number of theoretically possible genotypes is completely arbitrary.Several approaches have been described to infer haplotype phases in regions with CNAV, such as MOCSphaser, CNVphaser and polyHap. These approaches either treat copy number variation of genes as extra alleles, residing on two chromosomes (non-internal phasing), or they assume multiple pseudo-chromosomes har […]


A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data

EURASIP J Bioinform Syst Biol
PMCID: 4017783
PMID: 24868199
DOI: 10.1186/1687-4153-2014-7

[…] nformation about the total copies on a chromosome that could be potentially useful, it does not provide information on the diplotypes themselves.Another algorithm recently proposed by Kato et al. [], CNVphaser uses an EM approach to perform inference. The core limitation of that method is that the inference is performed within a CNV region and that the ploidy is considered fixed for an individual […]


A method for calling copy number polymorphism using haplotypes

Front Genet
PMCID: 3780619
PMID: 24069028
DOI: 10.3389/fgene.2013.00165

[…] . MOCSphaser (Kato et al., ) infers CNV-SNP haplotypes using an expectation-maximization (EM) algorithm but only accommodates integer copy numbers in CNV regions and SNP genotypes in non-CNV regions. CNVphaser employed a hierarchical partition-ligation strategy to break down a longer region into smaller blocks and used the EM algorithm to estimate the “haplotypes” frequencies just as for the regul […]


Inferring Haplotypes of Copy Number Variations From High Throughput Data With Uncertainty

PMCID: 3276117
PMID: 22384316
DOI: 10.1534/g3.111.000174
call_split See protocol

[…] the other haplotype, or another) but the total numbers of the alleles A and G are known as two and one, respectively ().For that aim, we combined an algorithm of Kang et al. () with the algorithms of CNVphaser () and MOCSphaser () so that the proposed algorithm could incorporate likelihood values for total copy numbers and unphased genotypes into the framework of the expectation-maximization (EM) […]


Inference of chromosome specific copy numbers using population haplotypes

BMC Bioinformatics
PMCID: 3128032
PMID: 21605463
DOI: 10.1186/1471-2105-12-194

[…] Map project during simulation. The total copy numbers at one CNV is simulated by randomly pairing two copy numbers on two different X chromosomes.In order to compare the accuracy of our algorithm and CNVphaser [,], which outputs posterior probabilities of each copy number, we parsed the output files of CNVPhaser and picked up the diplotype configuration with highest probability for each individual […]


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CNVphaser institution(s)
SNP Research Center, RIKEN, Yokohama, Japan; Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
CNVphaser funding source(s)
Supported in part by JSPS.KAKENHI (20790269).

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