Genotype harmonizer specifications


Unique identifier OMICS_15382
Name Genotype harmonizer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.4.18
Stability Stable
Maintained Yes



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  • person_outline Patrick Deelen <>

Publication for Genotype harmonizer

Genotype harmonizer in publications

PMCID: 5217260
PMID: 28056824
DOI: 10.1186/s12864-016-3452-1

[…] (rsq < 0.3) for bamse data and info score < 0.3 for piama and inma data. all the genotypes were aligned to the giant release of 1000g to facilitate further data integration and meta-analysis by genotype harmonizer 1.4.9 []. we had genotype data for 114 inma samples, age 0-4/5 years, and for 181 piama and 49 bamse samples, age 4–8 years., the dmeqtl and meqtl analysis was performed using the […]

PMCID: 5130901
PMID: 27818087
DOI: 10.1016/j.celrep.2016.10.053

[…] and 518,980 variants passed quality control. for further imputation of this dataset, we aligned the strands and variant identifiers to the reference genome of the netherlands (gonl) dataset using genotype harmonizer. the phasing was performed with shapeit2 version 2 with the gonl as a reference panel. finally, the data were imputed using impute2 with the gonl as the reference panel. […]

PMCID: 4922056
PMID: 27350042
DOI: 10.1186/s13059-016-1000-6

[…] snps were measured per cohort (for data generation details see tigchelaar et al. [] for ll, deelen et al. [] for lls, willemsen et al. [] for ntr, and hofman et al. [] for rs), harmonized (genotype harmonizer []), and imputed (impute2 []) using gonl5 [] as reference. snps with an imputation info-score <0.5, hardy–weinberg equilibrium p value <10−4, call rate <95 % or minor […]

PMCID: 5391837
PMID: 26898941
DOI: 10.1016/j.jaut.2016.01.002

[…] next, this data was imputed based on the genome of the netherlands (gonl) reference panel [–]. the merged genotypes were pre-phased using shapeit2 [] and aligned to the gonl reference panel using genotype harmonizer [] ( in order to resolve strand issues. imputation was performed using impute2 [] version 2.3.0 against the gonl reference panel. we used […]

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Genotype harmonizer institution(s)
University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
Genotype harmonizer funding source(s)
This work was supported by BBMRI-NL, a research infrastructure financed by the Netherlands Organization for Scientific Research (NWO project 184.021.007), the European Union Seventh Framework Programme (FP7/2007-2013) under grant 261433 (BioSHaRE-EU), the LifeLines/Target and TI Food and Nutrition (TIFN GH001).

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