MOTIVATION: Versatile and efficient variant calling tools are needed to analyze large scale sequencing datasets. In particular, identification of copy number changes remains a challenging task due to their complexity, susceptibility to sequencing biases, variation in coverage data and dependence on genome-wide sample properties, such as tumor polyploidy or polyclonality in cancer samples. RESULTS: We have developed a new tool, Canvas, for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched and unmatched tumor-normal studies. In addition to variant calling, Canvas infers genome-wide parameters such as cancer ploidy, purity and heterogeneity. It provides fast and easy-to-run workflows that can scale to thousands of samples and can be easily incorporated into variant calling pipelines. AVAILABILITY AND IMPLEMENTATION: Canvas is distributed under an open source license and can be downloaded from https://github.com/Illumina/canvas CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We present Fuzzy Prophet, a probabilistic database tool for constructing, simulating and analyzing business scenarios with uncertain data. Fuzzy Prophet takes externally defined probability distribution (so called VG-Functions) and a declarative description of a target scenario, and performs Monte Carlo simulation to compute probability distribution of the scenario's outcomes. In addition, Fuzzy Prophet supports parameter optimization,where probabilistic models are parameterized and a large parameter space must be explored to find parameters that optimize or achieve a desired goal. Fuzzy Prophet's key innovation is to use 'fingerprints' that can identify parameter values producing correlated outputs of a user-provided stochastic function and to reuse computations across such values. Fingerprints significantly expedite the process of parameter exploration in offline optimization and interactive what-if exploration tasks.