AGAAT: Automated computational tool integrating different genotyping array and correctional methods for data analysis

Genotyping arrays are widely used in studying the genetics of complex diseases. Arrays with multi-ethnic markers enable population-scale and cost-effective genetic studies in underrepresented populations. But automated pipelines that convert raw data files into association results are lacking for these genotyping arrays. Also, combining variant files from multiple genotyping projects is difficult due to differences arising from multiple versions of standard file formats like Variant Calling Format (VCF). We have developed an automated tool named AGAAT (Automated Genotyping Array Analysis Tool) to overcome these problems. In addition to the automated pipelines for multi-ethnic arrays, we have added additional Python scripts for multiple testing correction using haplotype blocks, candidategene analysis, candidate-gene common-variant analysis and addition of 1000 genome phase-3 genotype counts to the controls, followed by case-control association analysis.