IPGWAS

Integrated Pipeline for Genome-Wide Association Studies

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

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