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SynthEx is a tool to detect copy number alteration (CNA) and to profile tumor heterogeneity in a variety of high-throughput sequencing data. The SynthEx algorithm uses "synthetic normal" to represent the target; Thus, it does not need a matched pair of samples as normals.


Oncology; Genetic variation; Sequencing


  • Operation: Variant detection; Copy number estimation
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux
  • License: GNU GPL >=v2
  • Cost: Free
  • Version name: 1.06
  • Credit: The National Cancer Institute (NCI) Breast SPORE program, the Breast Cancer Research Foundation, the National Institutes of Health (NIH)
  • Contact: mengjiechen _at_
  • Collection: -


Silva GO, Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M "SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol, 2017
PMID: 28390427
PMCID: PMC5385048

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