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bioRxiv2016

tHapMix: simulating tumour samples through haplotype mixtures

MotivationLarge-scale rearrangements and copy number changes combined with different modes of cloevolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable oriant calling tools and create well-calibrated benchmarks.\n\nResultsWe 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.\n\nAvailability and implementationtHapMix is distributed under an open source license and can be downloaded from https://github.com/Illumina/tHapMix.\n\nContactsivakhno@illumina.com\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

Bioinformatics↗

bioRxiv2016

Canvas: versatile and scalable detection of copy number variants

Motivation: Increased throughput and diverse experimental designs of large-scale sequencing studies necessi-tate versatile, scalable and robust variant calling tools. In particular, identification of copy number changes re-mains 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.\n\nResults: We have developed a new tool, Canvas, for identification of copy number changes from diverse se-quencing 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 simple to execute workflows that can scale to thousands of samples and can be easily incorporated into existing variant calling pipelines.\n\nAvailability: Canvas is distributed under an open source license and can be downloaded from https://github.com/Illumina/canvas.\n\nContact: eroller@illumina.com\n\nSupplementary information: Supplementary data are available at Bioinformatics online.

Bioinformatics↗