HLA-IMPUTER – HLA Imputation and Association analysis using Population-specific Reference Panels

HLA-IMPUTER

:: DESCRIPTION

HLA-IMPUTER implements the HIBAG algorithm for HLA allele imputation with different population specific reference panels, including a new Han Chinese reference panel derived from 10,689 samples.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Apr 1;35(7):1244-1246. doi: 10.1093/bioinformatics/bty730.
HLA-IMPUTER: an easy to use web application for HLA imputation and association analysis using population-specific reference panels.
Shen JJ, Yang C, Wang YF, Wang TY, Guo M, Lau YL, Zhang X, Sheng Y, Yang W.

minimac 2 2014.9.15 – Faster Genotype Imputation

minimac 2 2014.9.15

:: DESCRIPTION

minimac is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 minimac2

:: MORE INFORMATION

Citation:

minimac2: faster genotype imputation.
Fuchsberger C, Abecasis GR, Hinds DA.
Bioinformatics. 2014 Oct 22. pii: btu704.

DIST 1.0.0 / DISTMIX v0.2.0- Direct Imputation of summary STatistics for unmeasured SNPs /from mixed Ethnicity Cohorts

DIST 1.0.0 / DISTMIX v0.2.0

:: DESCRIPTION

DIST is a software program for directly imputing the normally distributed summary statistics of unmeasured SNPs in a GWAS/meta-analysis without first imputing subject level genotypes.

DISTMIX is a very fast and novel software program for Directly Imputing summary STatistics (two-tailed Z-scores) for unmeasured SNPs from MIXed ethnicity cohorts using measured SNP summary data (including cohort allele frequencies) from the cohorts and external reference populations such as 1000 Genomes data.

::DEVELOPER

DIST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DIST / DISTMIX

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 15;29(22):2925-7. doi: 10.1093/bioinformatics/btt500. Epub 2013 Aug 28.
DIST: direct imputation of summary statistics for unmeasured SNPs.
Lee D1, Bigdeli TB, Riley BP, Fanous AH, Bacanu SA.

DISTMIX: Direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts.
Lee D, Bigdeli TB, Williamson VS, Vladimirov VI, Riley BP, Fanous AH, Bacanu SA.
Bioinformatics. 2015 Jun 9. pii: btv348.

FAPI 0.1 – Fast and Accurate P-value Imputation for Genetic Association

FAPI 0.1

:: DESCRIPTION

FAPI is a powerful multi-thread Java-based application developed to infer p-values of untyped Single-nucleotide polymorphisms (SNPs) through p-values of SNPs in LD with the untyped one. With similar imputation accuracy to other genotype imputation tools (including IMPUTEand MACH), FAPI is superfast, without requiring phases of reference genotypes and any sample raw genotypes.

::DEVELOPER

Miao-xin Li, The University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

  FAPI

:: MORE INFORMATION

Citation

Kwan JS, Li MX, Deng JE, Sham PC.
An ultra-fast and versatile p-value imputation for genome-wide association studies
(Submitted)

DISSCO 1.0 – Direct Imputation of Summary Statistics allowing COvariates

DISSCO 1.0

:: 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

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 DISSCO

:: 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.

MaCH-Admix 2.0.203 – Genotype Imputation for Admixed Populations or with Large Reference Panels

MaCH-Admix 2.0.203

:: DESCRIPTION

MaCH-Admix is a genotype imputation software that extends the capabilities of MaCH. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s).

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX

:: DOWNLOAD

 MaCH-Admix

:: MORE INFORMATION

Citation

MaCH-admix: genotype imputation for admixed populations.
Liu EY, Li M, Wang W, Li Y.
Genet Epidemiol. 2013 Jan;37(1):25-37. doi: 10.1002/gepi.21690. Epub 2012 Oct 16.

GIGI 1.06.1 – Genotype Imputation Given Inheritance

GIGI 1.06.1

:: DESCRIPTION

GIGI is a computer program to impute missing genotypes on pedigrees.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GIGI

:: 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

famSKAT-RC 20140725 – Combining Family- and Population-based Imputation data for Association analysis of Rare and common Variants in large Pedigrees

famSKAT-RC 20140725

:: 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

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 famSKAT-RC

:: 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.

HIBAG 1.4.0 – HLA Genotype Imputation with Attribute Bagging

HIBAG 1.4.0

:: 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

Xiuwen Zheng (zhengx@u.washington.edu) , Bruce Weir (bsweir@u.washington.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R
  • BioConductor

:: DOWNLOAD

 HIBAG

:: 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.