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Summary Reference genomes are refined to reflect error corrections and other improvements. While this process improves novel data generation and analysis, incorporating data analyzed on an older reference genome assembly requires transforming the coordinates and representations of the data to the new assembly. Multiple tools exist to perform this transformation for coordinate-only data types, but none supports accurate transformation of genome-wide short variation. Here we present GenomeWarp, a tool for efficiently transforming variants between genome assemblies. GenomeWarp transforms regions and short variants in a conservative manner to minimize false positive and negative variants in the target genome, and converts over 99% of regions and short variants from a representative human genome. Availability and implementation GenomeWarp is written in Java. All source code and the user manual are freely available at https://github.com/verilylifesciences/genomewarp. Supplementary information Supplementary data are available at Bioinformatics online.

Summary: Here, we present ContEst, a tool for estimating the level of cross-individual contamination in next-generation sequencing data. We demonstrate the accuracy of ContEst across a range of contamination levels, sources and read depths using sequencing data mixed in silico at known concentrations. We applied our tool to published cancer sequencing datasets and report their estimated contamination levels. Availability and Implementation: ContEst is a GATK module, and distributed under a BSD style license at http://www.broadinstitute.org/cancer/cga/contest Contact: kcibul@broadinstitute.org; gadgetz@broadinstitute.org Supplementary information: Supplementary data is available at Bioinformatics online.