Tag: Imputation

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.

AlphaFamImpute 0.0.1 – Imputation in full-sib families from Genotype-by-sequencing data

AlphaFamImpute 0.0.1

:: DESCRIPTION

AlphaFamImpute is a genotype calling, phasing, and imputation algorithm for large full-sib families in diploid plants and animals which supports individuals genotyped with SNP array or GBS data. The approach draws heavily on single and multi-locus iterative peeling (as in AlphaPeel). It also has been inspired by work outside our group such as hs-phase (Ferdosi et al. 2014), and magicimpute (Zheng et al. 2018).

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

AlphaFamImpute

:: MORE INFORMATION

Citation

Whalen A, Gorjanc G, Hickey JM.
AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data.
Bioinformatics. 2020 Aug 1;36(15):4369-4371. doi: 10.1093/bioinformatics/btaa499. PMID: 32467963; PMCID: PMC7520044.

Ezimputer v3 – A workflow for Parallelized Genome Wide Imputation

Ezimputer v3

:: DESCRIPTION

The EZImputer workflow is a modular set of scripts for genome-wide imputation. It automates many of the steps regularly needed for an imputation project.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 EZImputer

:: MORE INFORMATION

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

Precision Medicine Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

  FAPI

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2016 May;24(5):761-6. doi: 10.1038/ejhg.2015.190. Epub 2015 Aug 26.
FAPI: Fast and accurate P-value Imputation for genome-wide association study
Johnny S H Kwan, Miao-Xin Li, Jia-En Deng , Pak C Sham

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.

SKNN 1.0.1 – Sequential K-Nearest Neighbor method for Microarray data Imputation

SKNN 1.0.1

:: DESCRIPTION

SKNN (SeqKnn) imputes the missing values sequentially from the gene having least missing values, and uses the imputed values for the later imputation

:: DEVELOPER

Bioinformatics and Synthetic Biology Lab, KAIST.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 SKNN

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2004 Oct 26;5:160.
Reuse of imputed data in microarray analysis increases imputation efficiency.
Kim KY, Kim BJ, Yi GS.