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Quality control software tools | Genome-wide association analysis

GWAS result files are prone to errors due to the vast amount of data they contain and the different manner in which these data are generated by individual cohorts. Before combining data from individual studies in a meta-analysis, it is important to…
lodGWAS
Desktop

lodGWAS

An appropriate statistical method for genome-wide association study analysis of…

An appropriate statistical method for genome-wide association study analysis of biomarkers whose measurements are constrained by limits of detection. lodGWAS depends upon the “survival” R…

QCGWAS
Desktop

QCGWAS Quality Control of Genome Wide Association Study results

An R package that automates the quality control of genome-wide association…

An R package that automates the quality control of genome-wide association result files. Its main purpose is to facilitate the quality control of a large number of such files before meta-analysis.…

EasyQC
Desktop

EasyQC

Provides advanced functionality (i) to perform file-level quality control (QC)…

Provides advanced functionality (i) to perform file-level quality control (QC) of single genome-wide association (GWA) data-sets; (ii) to conduct quality control across several GWA data-sets…

PBAP
Desktop

PBAP

A pedigree-based analysis pipeline suite of programs geared towards SNPs and…

A pedigree-based analysis pipeline suite of programs geared towards SNPs and sequence data. PBAP performs quality control, marker selection and file preparation. PBAP sets up files for MORGAN, which…

repfdr
Desktop

repfdr

Estimates Bayes and local Bayes false discovery rates (FDR) for replicability…

Estimates Bayes and local Bayes false discovery rates (FDR) for replicability analysis. Repfdr provides a way of performing analysis and theoretical justifications. This approach is a general method…

GWASTools
Desktop

GWASTools

An R/Bioconductor package for quality control and analysis of genome-wide…

An R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS.…

PhenoMan
Desktop

PhenoMan

Provides approaches for efficient exploration and management of phenotype data.…

Provides approaches for efficient exploration and management of phenotype data. Proper QC of phenotypes before proceeding to the association analysis is critical to ensure control of type I and II…

GWAtoolbox
Desktop

GWAtoolbox

An R-package for fast quality control and data handling of multiple data files…

An R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS). Thought to be employed as a preprocessing tool in the…

GTOOL
Desktop

GTOOL

A program for transforming sets of genotype data for use with the programs…

A program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. GTOOL can be used to 1) generate subsets of genotype data, 2) to convert genotype data between the PED…

QCTOOL
Desktop

QCTOOL

A typical use of QCTOOL is to compute per-sample and per-SNP summary statistics…

A typical use of QCTOOL is to compute per-sample and per-SNP summary statistics for a cohort, and use these to filter out samples and SNPs (either by removing them from the files or by writing…

Goldsurfer
Desktop

Goldsurfer

Allows users to proceed genome wide association studies (GWAS). Goldsurfer is a…

Allows users to proceed genome wide association studies (GWAS). Goldsurfer is a standalone software that can be used for managing a complete GWA project. It is able to analyze results from publicly…

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