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A tool to simulate haplotype-phased allele-specific copy number variation (CNV) into a Binary Alignment Mapping (BAM) and cancer CNVs in exome and targeted cell-free DNA sequencing data.


Genetics; genetic variation


  • Operation: Modelling and simulation
  • Input: BAM, two lists of non- overlapping genomic coordinates for allele-specific gains and losses
  • Output: -
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Apache License 2.0
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: The Princess Margaret Cancer Foundation, Canada Research Chairs Program, Cancer Research Society, Canadian Neuroendocrine Tumour Society, Canada Foundation for Innovation, Leaders Opportunity Fund, and the Ontario Ministry of Research and Innovation, Ontario Research Fund Small Infrastructure Program.
  • Contact: Trevor J. Pugh trevor.pugh _at_
  • Collection: -


Samadian S, Bruce JP, Pugh TJ "Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets." PLoS Comput Biol. 2018 Mar 28;14(3):e1006080. eCollection 2018 Mar.
PMID: 29590101
PMCID: PMC5891060

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