:: DESCRIPTION
tagIMPUTE (Tag-based imputation) is a command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hu, Y. J. and Lin, D. Y. (2010),
“Analysis of Untyped SNPs: Maximum Likelihood and Imputation Methods“,
Genet Epidemiol. 2010 Dec;34(8):803-15.
:: DESCRIPTION
The genipe module includes a script (named genipe-launcher) that automatically runs a genome-wide imputation pipeline using Plink, shapeit and impute2.
::DEVELOPER
Marie-Pierre Dubé’s Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
enipe
:: MORE INFORMATION
Citation
Lemieux Perreault LP, Legault MA, Asselin G, Dubé MP.
genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.
Bioinformatics. 2016 Dec 1;32(23):3661-3663. doi: 10.1093/bioinformatics/btw487. Epub 2016 Aug 6. PMID: 27497439; PMCID: PMC5181529.
:: DESCRIPTION
FISH is a java program for fast and accurate diploid genotype imputation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 31. [Epub ahead of print]
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model.
Zhang L1, Pei YF, Fu X, Lin Y, Wang YP, Deng HW.
:: DESCRIPTION
hsphase is an R package that implements a very fast method for phasing, sire genotype imputation, identification of paternal strand of origin and recombination events in half-sib families
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2014 Jun 7;15:172. doi: 10.1186/1471-2105-15-172.
hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups.
Ferdosi MH1, Kinghorn BP, van der Werf JH, Lee SH, Gondro C.
:: 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
ImpG-Summary is a software package implementing methods for imputation from summary statistics and accompanying data. The software takes as input 1000 Genomes reference haplotypes and summary association statistics at a typed set of SNPs from a GWAS or meta-analysis. It outputs summary association statistics at all 1000 Genomes variants.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.
Pasaniuc B, Zaitlen N, Shi H, Bhatia G, Gusev A, Hirschhorn J, Strachan DP, Patterson N, Price AL.
Bioinformatics. 2014 Jul 1. pii: btu416
:: DESCRIPTION
famSKAT-RC is an R scripts to carry out a combined rare- and common-variant gene-based test of association in the presence of related individuals.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genet Epidemiol. 2014 Nov;38(7):579-90. doi: 10.1002/gepi.21844. Epub 2014 Aug 1.
Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees.
Saad M1, Wijsman EM.
:: 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
:: DESCRIPTION
PBLR is an effective tool to recover dropout events on both simulated and real datasets,and can dramatically improve low-dimensional representation and reveal gene-gene relationship compared to several state-of-the-art methods.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang L, Zhang S.
Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts.
J Mol Cell Biol. 2021 Apr 10;13(1):29-40. doi: 10.1093/jmcb/mjaa052. PMID: 33002136; PMCID: PMC8035992.
:: DESCRIPTION
DISSCO is a JAVA application for direct imputation of summary statistics allowing for covariates.
::DEVELOPER
Yun Li Statistical Genetics Group
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DISSCO: Direct Imputation of Summary Statistics allowing COvariates.
Xu Z, Duan Q, Yan S, Chen W, Li M, Lange E, Li Y.
Bioinformatics. 2015 Mar 24. pii: btv168.