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).
Features
- genome-wide association study (GWAS)
- quality control (qc)
- Manhattan plot and QQ plot
- Cochran-Armitage trend test, Association test
- combine GWAS dataset, Split GWAS Data by Chromosome
- Convert EIGENSTRAT output chi-square to p value
- Convert MACH imputation output to PED/MAP format and SNPTEST format
- Convert PED/MAP files to the default input format of PHASE and BEAGLE
- Convert PLINK and SNPTEST files to GWAMA format
- P-Value Calculator (Chi-square test, Cochran-Armitage trend test, and Fisher’s exact test)
- Change affection status of GWAS data
- filt Subjects of GWAS data by affection status (case/control) and/or gender (male/female)
- GUI for PLINK, SNP ratio Test
- filter singleton significant SNPs
- eigPlot (plot the eigenstrat result)
- Convert PED/MAP files to the default input format of MACH and IMPUTE2
- Convert IMPUTE2 imputation output to TPED/TFAM (PLINK) format
IPGWAS is available at sourceforge.