| category Bioinformatics  | tag GWAS  Perl 

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).

  • 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.

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