tHapMix: simulating tumour samples through haplotype mixtures.
Large-scale rearrangements and copy number changes combined with different modes of clonal evolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable variant calling tools and create well-calibrated benchmarks.



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.



tHapMix is distributed under an open source license and can be downloaded from https://github.com/Illumina/tHapMix CONTACT: sivakhno@illumina.comSupplementary information: Supplementary data are available at Bioinformatics online.
Chesterford Research Park, Illumina Cambridge Ltd, Little Chesterford, CB10 1XL, UK.
Sergii
S
Ivakhno
Chesterford Research Park, Illumina Cambridge Ltd, Little Chesterford, CB10 1XL, UK.
Camilla
C
Colombo
Illumina Inc, San Diego, CA 92122, USA.
Stephen
S
Tanner
Chesterford Research Park, Illumina Cambridge Ltd, Little Chesterford, CB10 1XL, UK.
Philip
P
Tedder
Chesterford Research Park, Illumina Cambridge Ltd, Little Chesterford, CB10 1XL, UK.
Stefano
S
Berri
Chesterford Research Park, Illumina Cambridge Ltd, Little Chesterford, CB10 1XL, UK.
Anthony J
AJ
Cox
D003198:Computer Simulation; D056915:DNA Copy Number Variations; D004273:DNA, Neoplasm; D016678:Genome; D023281:Genomics / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D011003:Ploidies; D012984:Software
D004273:DNA, Neoplasm