title: IPGWAS: an integrated pipeline for rational quality control and association analysis of genome-wide genetic studies.
abstract: Large numbers of samples and marker loci were tested for association in genome-wide association studies (GWAS). Hence, quality control (QC) by removing individuals or markers with low genotyping quality is of utmost importance to minimize potential false positive associations. IPGWAS was developed to facilitate the identification of the rational thresholds in QC of GWAS datasets, association analysis, Manhattan plot, quantile-quantile (QQ) plot, and format conversion for genetic analyses, such as meta-analysis, genotype phasing, and imputation. IPGWAS is a multiplatform application written in Perl with a graphical user interface (GUI) and available for free at http://sourceforge.net/projects/ipgwas/.
authors.affiliation: Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong. nolanfyh@gmail.com
authors.forename: Yan-Hui
authors.initials: YH
authors.lastname: Fan
authors.forename: You-Qiang
authors.initials: YQ
authors.lastname: Song
mesh_terms: D005189:False Positive Reactions; D055106:Genome-Wide Association Study; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D012984:Software