The Genotype Phenotype Association Toolkit (GPAT) Applications in Population Genomics

Current generation sequencing technologies have made population genomic analyses for non-model organisms a reality.  Genome sequencing of populations generates large variant call sets that pose a number of challenges to traditional population genetics.  Missing genotypes, genotyping error, and data management often preclude informative analyses.  We have addressed these challenges by developing the Genotype Phenotype Association Toolkit (GPAT).  GPAT provides an integrated suite of tools designed specifically to work with NGS data.  GPAT’s command line options allow powerful customization for both data analysis and visualization.  In addition, GPAT has a simple, intuitive API that facilitates rapid software development, and is accessible even for entry-level programmers. We present several applications of GPAT to real world data, demonstrating  its utility for  genotype-phenotype association using several non-model organism populations.