Copy Number Estimation from Tumor Genome Sequencing Data

Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.


Changes in version 3.0.0 (2019-05-09)

  • Code cleanup and refactoring
  • Bug fixes
  • Use readr and stop relying on system commands (grep, sed, gunzip) to read seqz files
  • Use the package pbapply for progress bar
  • Normalize each sample separately
  • Provide coverage profile of the 2 samples separately, before and after normalization
  • Provide CG-content vs depth profile for each samples, before and after normalization
  • Draw standard "mirrored" BAF (from 0 to 1) in the raw genome view

Changes in version 2.1.2 (2015-08-18)

  • Keep the order of the bases corresponding to the major and minor alleles as in the normal sample. (allows mocking haplotype).
  • Fix check for NOTES in newer R versions

Changes in version 2.1.1 (2015-01-20)

  • Fix heterozygous detection when importing VarScan2 data of very high coverage seq.
  • Cleanup
  • Update citation info to published manuscript

Changes in version 2.1.0 (2014-10-08)

  • Add function bam2seqz
  • Add raw data depth-ratio/Bf in the genome view plots
  • Results model fitting plot using the B-allele/depth-ratio plot.
  • Present alternative solutions using local maxima of the CP plot.
  • Model the expected B-allele frequencies with a t-distribution using the observed sd, rather then taking the 95% of the observed Bf.
  • Use dt instead of dbinom for the BAF and depth ratio model.
  • Fix documentation discrepancies on the execution.
  • Add breaks as optional argument - enables to input custom segmentation -
  • Add different segmentation options, fast, het and full, corresponding to different resolutions.
  • Minor fixes.

Changes in version 2.0.0 (2014-04-08)

  • Change seqz names header and some function arguments/formats to improve usability
  • Add to a method argument to calculate cellularity and ploidy also from mutations
  • Change the recommended file extension from ".abfreq" to ".seqz" for clarity.
  • The "seqz" file now contains a column with strand orientation information.
  • "cp.plot" now plots the scaled log-likelihood.
  • "theoretical.depth.ratio" now implements the correct formula.
  • The "theoretical.*" functions have their arguments rearranged, and defaults changed, for consistency.
  • "sequenza.extract" now has additional filtering arguments.
  • Miscellaneous cleanup/simplification/optimization.

Changes in version 1.0.5 (2014-02-04)

  • Add a python utility for binning the data to a desired window size (reducing vastly memory footprint in the analysis)
  • Fix default workflows parameter to detect CN up to 20.

Changes in version 1.0.4 (2014-01-16)

  • Add function to import VarScan2 output
  • Add results function, to save results and standard plots.
  • Fix error on loading non-zipped files in the workflow.
  • Ignore error and finish the process if one of the chromosome fails in the workflows.

Changes in version 1.0.3 (2013-12-12)

  • Fix grep instructions that broke single chromosome loading

Reference manual

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3.0.0 by Francesco Favero, a year ago, Mailing list:!forum/sequenza-user-group

Report a bug at

Browse source code at

Authors: Francesco Favero [aut, cre] , Andrea Marion Marquard [rev] , Tejal Joshi [rev] , Aron Charles Eklund [aut, ths]

Documentation:   PDF Manual  

GPL-3 license

Imports pbapply, squash, iotools, readr, seqminer, copynumber

Suggests testthat, knitr, rmarkdown, rmdformats

System requirements: pandoc (>= 1.12.3)

See at CRAN