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A tool for detection of single nucleotide polymorphism (SNP) and short insertions and deletions (indels) in data from single-cell sequencing.


Genetic variation; DNA polymorphism


  • Operation: Indel detection; SNP detection
  • Input: BAM, FASTA, VCF
  • Output: -
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: LInux; Mac OS X; Microsoft Windows
  • License: GNU Affero General Public License version 3 or later
  • Cost: Free
  • Version name: 2.0.0
  • Maturity: Mature
  • Credit: The National Institutes of Health (NIH)
  • Contact: Xiao Dong biosinodx _at_, xiao.dong _at_ | Yujue Wang spsc83 _at_
  • Collection: -


Dong X, Zhang L, Milholland B, Lee M, Maslov AY, Wang T, Vijg J "Accurate identification of single-nucleotide variants in whole-genome-amplified single cells." Nat Methods. 2017 May;14(5):491-493.
PMID: 28319112
PMCID: PMC5408311

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