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Zinfandel is a tool designed for detection of copy number variation (CNV) in low coverage data. It uses Hidden Markov Model (HMM) to estimate the coverage from multiple mate-pairs without designating single mate-pairs as outliers.


Whole genome sequencing; Genetics; Genetic variation


  • Operation: Copy number estimation
  • Input: FASTA; Mapview; Parameter file
  • Output: -
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: 0.9
  • Credit: NSF CAREER 0845677 and NIH U54CA121852, International Serious Adverse Event Consortium.
  • Contact: yshen _at_
  • Collection: -


Shen Y, Gu Y, Pe'er I "A hidden Markov model for copy number variant prediction from whole genome resequencing data." BMC Bioinformatics. 2011;12 Suppl 6:S4.
PMID: 21989326
PMCID: PMC3194192

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