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ichorCNA is an R tool for estimation of tumor fractions in ultra-low pass whole genome sequencing (WGS) and prediction of large-scale copy number variation (CNV). The ichorCNA algorithm uses a hidden Markov model (HMM) for the probabilistic modeling and works in sequencing coverages down to 0.1X.


Genetics; Molecular genetics; Genetic variation; DNA structural variation; Medicine; Oncology


  • Operation: Analysis; Sequence analysis; Copy number estimation
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 0.1.0
  • Maturity: Stable
  • Credit: Gerstner Family Foundation, Canadian Institutes for Health Research Postdoctoral Fellowship, Stand Up To Cancer—Prostate Cancer Foundation Prostate Dream Team, American Association for Cancer Research, anssen Pharmaceuticals, Inc., Koch Institute, Paul C. Zamecnik, MD, Chair in Oncology at Massachusetts General Hospital.
  • Contact: ichorcna _at_,!forum/ichorcna
  • Collection: -


Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, Stewart C, Rosenberg M, Francis JM, Zhang CZ, Cohen O, Oh C, Ding H, Polak P, Lloyd M, Mahmud S, Helvie K, Merrill MS, Santiago RA, O'Connor EP, Jeong SH, Leeson R, Barry RM, Kramkowski JF, Zhang Z, Polacek L, Lohr JG, Schleicher M, Lipscomb E, Saltzman A, Oliver NM, Marini L, Waks AG, Harshman LC, Tolaney SM, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Johannessen CM, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Love JC, Meyerson M "Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors." Nat Commun. 2017 Nov 6;8(1):1324.
PMID: 29109393
PMCID: PMC5673918

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