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).
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).
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
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.
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.
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.