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YMAP is a pipeline for detection and analysis of custom copy number variation (CNV), single nucleotide polymorphism (SNP) and loss of heterozygosity (LOH). YMAP makes figures, a summary of the analyses and displays them on a web page.


Genetics; genetic variation; model organisms; pathogens


  • Operation: Visualisation; data retrieval; variant detection
  • Input: FASTQ
  • Output: -
  • Software interface: Command-line user interface; web user interface
  • Language: Python;Javascript;PHP
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: The MIT License
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: The National Science Foundation, the CIFAR Genetic Networks Program, NIH Pre-Doctoral Training Grant, Human Frontiers Science Program, the Howard Hughes Medical Institute, the Burroughs Wellcome Fund, a National Institutes of Health PIONEER award, Sloan Fellowship, the National Institute of Allergy and Infectious Diseases (NIAID), the People Programme (Marie Curie Actions), the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement number 303635 and an ERC Advanced Award.
  • Contact: ymapsupport _at_
  • Collection: -


Abbey DA, Funt J, Lurie-Weinberger MN, Thompson DA, Regev A, Myers CL, Berman J "YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens." Genome Med. 2014 Nov 20;6(11):100. 2014.
PMID: 25505934
PMCID: PMC4263066

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