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EasyQC specifications


Unique identifier OMICS_11041
Name EasyQC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 9.2
Stability Stable
Cairo, plotrix, data.table
Maintained Yes


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  • person_outline Lauri Eronen <>

Publication for EasyQC

EasyQC in publications

PMCID: 5560754
PMID: 28787443
DOI: 10.1371/journal.pgen.1006925

[…] plots, using populations from the 1000 genomes project to anchor these analyses. prior to performing meta-analyses of the association results provided by each participating study, we ran the easyqc protocol [] to check for population allele frequency deviations and proper trait transformation in each cohort. in terms of hematological phenotypes, we excluded individuals with blood cancer, […]

PMCID: 5407576
PMID: 28448500
DOI: 10.1371/journal.pgen.1006528

[…] (), cases and controls were analyzed separately., all study-specific files for the three regression models listed above were processed through a standardized quality control protocol using the easyqc software []. the study-specific quality control measures included checks on file completeness, range of test statistics, allele frequencies, trait transformation, population stratification, […]

PMCID: 5231365
PMID: 28081215
DOI: 10.1371/journal.pone.0169873

[…] four pcas. these analysis were performed using the r package []., the quality control of the gwas summary statistics from harvard cohorts and the fhs gwas summary statistics was performed using the easyqc software []. after quality control there were 9,001,799 markers from harvard cohorts and 8,246,930 markers from fhs. the cleaned files of both datasets (harvard cohorts and fhs) […]

PMCID: 5179953
PMID: 27412012
DOI: 10.1093/hmg/ddw211

[…] l accounting for familial dependencies described by a pedigree-based kinship matrix., quality control and filtering of snps was performed centrally and standardized by the innsbruck study group using easyqc (). snps were only included in the analysis if they fulfilled the following criteria: imputation quality ≥0.4 (e.g. impute info), minor allele frequency ≥1% and a p-value of the hwe-test ≥ 1×10 […]

PMCID: 4884152
PMID: 27089181
DOI: 10.1038/ng.3552

[…] sample size of 298,420 individuals. before meta-analysis, a uniform set of quality-control (qc) procedures were applied to the cohort-level summary statistics, including but not limited to the easyqc protocol. all analyses were restricted to european-ancestry individuals., we performed a sample-size-weighted meta-analysis of the cohort-level summary statistics. to adjust standard errors […]

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EasyQC institution(s)
Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany

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