ipgwas online with Winfy

We have hosted the application ipgwas in order to run this application in our online workstations with Wine or directly.

Quick description about 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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