GSR: Simulator - VarSim
|Short Description||A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications|
|Long Description||VarSim is a framework for assessing alignment and variant calling accuracy in high-throughput genome sequencing through simulation or real data. In contrast to simulating a random mutation spectrum, it synthesizes diploid genomes with germline and somatic mutations based on a realistic model. This model leverages information such as previously reported mutations to make the synthetic genomes biologically relevant. VarSim simulates and validates a wide range of variants, including single nucleotide variants, small indels and large structural variants. It is an automated, comprehensive compute framework supporting parallel computation and multiple read simulators. Furthermore, we developed a novel map data structure to validate read alignments, a strategy to compare variants binned in size ranges and a lightweight, interactive, graphical report to visualize validation results with detailed statistics. Thus far, it is the most comprehensive validation tool for secondary analysis in next generation sequencing.|
|Last Release||6 months ago|
|Citations||Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY, VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications., Bioinformatics, 05-01-2015 [ Abstract, cited in PMC ]|
|GSR Certification||This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.|
|Author verification||The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.|
|Type of Simulated Data|
|Population Size Changes|
No example publication using VarSim has been provided.
Please propose new citations if you are aware of publications that use this software.