bcbio-variation is a toolkit to analyze genome variation data, built on top of the Genome Analysis Toolkit (GATK) with Clojure. It supports scoring for the Archon Genomics X PRIZE competition and is also a general framework for variant file comparison. It enables validation of variants and exploration of algorithm differences between calling methods by automating the process involved with comparing two sets of variants. For users, this integrates with the bcbio-nextgen framework to automate variant calling and validation. For developers, bcbio.variation provides command line tools and an API to clean and normalize variant data in VCF format avoiding comparison artifacts associated with different variant representations.