tHapMix: simulating tumour samples through haplotype mixtures.

Motivation: Large-scale rearrangements and copy number changes combined with different modes of clo evolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable v iant calling tools and create well-calibrated benchmarks. Results: We developed a new simulation framework tHapMix that enables the creation of tumour samples with different ploidy, purity and polyclonality features. It easily scales to simulation of hundreds of somatic genomes, while re-use of real read data preserves noise and biases present in sequencing platforms. We further demonstrate tHapMix utility by creating a simulated set of 140 somatic genomes and showing how it can be used in training and testing of somatic copy number variant calling tools. Availability and implementation: tHapMix is distributed under an open source license and can be downloaded from https://github.com/Illumina/tHapMix . Contact: sivakhno@illumina.com Supplementary information: Supplementary data are available at Bioinformatics online.