This is the Linux app named IPGWAS whose latest release can be downloaded as ipgwas3.0.5.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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DESCRIPTIONIntegrated Pipeline for Genome-Wide Association Studies
- 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
This is an application that can also be fetched from https://sourceforge.net/projects/ipgwas/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.