:: DESCRIPTION
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data.
Bellos E, Coin LJ.
Bioinformatics. 2014 Sep 1;30(17):i639-i645.
:: DESCRIPTION
VarGeno is a method for SNP genotyping from Illumina whole genome sequencing data. VarGeno builds upon LAVA by improving the speed of k-mer querying as well as the accuracy of the genotyping strategy.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics, 35 (3), 415-420 2019 Feb 1
Toward Fast and Accurate SNP Genotyping From Whole Genome Sequencing Data for Bedside Diagnostics
Chen Sun , Paul Medvedev
:: DESCRIPTION
Aldy is a computational tool that performs allelic decomposition of highly polymorphic, multi-copy genes through using whole or targeted genome sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nat Commun, 9 (1), 828 2018 Feb 26
Allelic Decomposition and Exact Genotyping of Highly Polymorphic and Structurally Variant Genes
Ibrahim Numanagić et al.
:: DESCRIPTION
CNVnator is a tool for Copy number variation (CNV) discovery and genotyping from depth of read mapping.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Abyzov A, Urban AE, Snyder M, Gerstein M.
Genome Res. 2011 Jun;21(6):974-84. Epub 2011 Feb 7.
:: DESCRIPTION
hzAnalyzer is a new R package that we have developed for detection, quantification, and visualization of homozygous segments/ROH in high-density SNP datasets.
::DEVELOPER
Laboratory for Medical Science Mathematics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2011;12(3):R21. doi: 10.1186/gb-2011-12-3-r21. Epub 2011 Mar 11.
hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets.
Johnson TA, Niimura Y, Tanaka H, Nakamura Y, Tsunoda T.
:: DESCRIPTION
DetSex is a software to assign marker to their chromosome type and to perform sexing of individuals using genotyping data.
::DEVELOPER
Centre de Biologie et Gestion des Populations (CBGP)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Ecol Resour. 2014 Nov;14(6):1141-59. doi: 10.1111/1755-0998.12264. Epub 2014 May 14.
Using genotyping data to assign markers to their chromosome type and to infer the sex of individuals: a Bayesian model-based classifier.
Gautier M
:: DESCRIPTION
The Resilience Project aims at finding individuals with rare genetic mutations that the medical text books would indicate should have caused catastrophic illness but somehow these individuals are “resilient” – they have been protected via yet to be discovered genetic or environmental factors.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ebGenotyping is a novel statistical model to fit the observed non-reference allele frequency data, and utilize the empirical Bayes method for both genotyping and SNP detection, where an ECM algorithm is implemented to estimate the model parameters.
::DEVELOPER
Na You and Gongyi Huang <53hgy at 163.com>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
An Empirical Bayes Method for Genotyping and SNP Detection Using Multi-sample Next-generation Sequencing Data.
Huang G, Wang S, Wang X, You N.
Bioinformatics. 2016 Jul 4. pii: btw409.
:: DESCRIPTION
Affy6CNV is a pipeline for calling CNVs from Affymetrix 6.0 genotyping array data.
::DEVELOPER
Conrad Lab | Washington University Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GenoSNP is a genotyping algorithm for the Illumina Infinium SNP genotyping assay [1]. It is entirely within-sample and does not require the need for a population of control samples nor parameters derived from such a population. The ability to call genotypes using only within-sample information makes the method computationally light and practical for studies involving rare variants and small sample sizes.
::DEVELOPER
Eleni Giannoulatou at eleni@well.ox.ac.uk
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A Variational Bayes within-sample SNP genotyping algorithm that does not require a reference population.
Giannoulatou E, Yau C, Colella S, Ragoussis J, Holmes CC.
Bioinformatics. 2008 Oct 1;24(19):2209-14
