:: DESCRIPTION
Reveel is an ultrafast tool for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Reveel: large-scale population genotyping using low-coverage sequencing data.
Huang L, Wang B, Chen R, Bercovici S, Batzoglou S.
Bioinformatics. 2015 Sep 9. pii: btv530.
:: DESCRIPTION
GENOSIM is a set of programs to simulate genotypes, breeding values, phenotypes, and DNA sequence read depth and to resolve SNP conflicts between parent and offspring genotypes
::DEVELOPER
Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
FINDHAP is a program to find haplotypes and impute genotypes from multiple marker sets and sequence data
::DEVELOPER
Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Dairy Sci. 2013 Jan;96(1):668-78. doi: 10.3168/jds.2012-5702. Epub 2012 Oct 11.
Genomic imputation and evaluation using high-density Holstein genotypes.
VanRaden PM1, Null DJ, Sargolzaei M, Wiggans GR, Tooker ME, Cole JB, Sonstegard TS, Connor EE, Winters M, van Kaam JB, Valentini A, Van Doormaal BJ, Faust MA, Doak GA.
:: DESCRIPTION
The iConvert program allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A.
BMC Genomics. 2015 Apr 10;16(1):283.
:: DESCRIPTION
dbVOR is a database system for importing pedigree, phenotype and genotype data and exporting selected subsets.
::DEVELOPER
Division of Statistical Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets
Baron RV, Conley YP, Gorin MB, Weeks DE.
BMC Bioinformatics. 2015 Mar 18;16(1):91.
:: DESCRIPTION
HIBAG is a state of the art software package for imputing HLA types using SNP data, and it uses the R statistical programming language. HIBAG is highly accurate, computationally tractable, and can be used by researchers with published parameter estimates (provided for subjects of European, Asian, Hispanic and African ancestries) instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles deduced using bootstrap aggregating and random subsets of variables.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
X. Zheng, J. Shen, C. Cox, J. Wakefield, M. Ehm, M. Nelson, B. Weir.
HIBAG – HLA Genotype Imputation with Attribute Bagging
Pharmacogenomics J. 2013 May 28. doi: 10.1038/tpj.2013.18.
:: DESCRIPTION
The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Res Notes. 2014 Dec 11;7:901. doi: 10.1186/1756-0500-7-901.
Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration.
Deelen P1, Bonder MJ, van der Velde KJ, Westra HJ, Winder E, Hendriksen D, Franke L, Swertz MA.
:: DESCRIPTION
The GIST (Genotype-IBD Sharing Test) is a method for detecting association between marker genotypes and IBD sharing at the same locus. Such an association will indicate that the marker itself, or one in linkage disequilibrium with it, could account for the observed linkage signal (at least partially). The software can be used to analyze affected sibship data.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li C, Scott LJ, Boehnke M. (2004)
Assessing Whether an Allele Can Account in Part for a Linkage Signal: The Genotype-IBD Sharing Test (GIST).
Am. J. Hum. Genet. 74:418-431
:: DESCRIPTION
GIGI is a computer program to impute missing genotypes on pedigrees.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2013).
GIGI: An approach to effective imputation of dense genotypes on large pedigrees.
American Journal of Human Genetics 92:504-516
