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A tool for analysis and visualization of allele-specific copy number variation (CNV) and loss-of-heterozygosity (LOH) in cancer genomes. The Patchwork tool comes in two variants, Patchwork which takes BAM files as input and PatchworkCG takes CompleteGenomics files as input.
Alternative name: patchworkCG.


Genomics; DNA structural variation; Visualisation


  • Operation: Copy number estimation
  • Input: BAM or CompleteGenomics
  • Output: -
  • Software interface: Command-line user interface; Library
  • Language: R;Perl;Python
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Maturity: Beta
  • Credit: Lions Cancer Fund and strategic ALF funding, Uppsala University Hospital, SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) and UPPMAX Next Generation Sequencing Cluster & Storage (UPPNEX).
  • Contact: sebastian.dilorenzo _at_ | anders.isaksson _at_ | markus.mayrhofer _at_
  • Collection: -


Chen H, Bell JM, Zavala NA, Ji HP, Zhang NR "Allele-specific copy number profiling by next-generation DNA sequencing." Nucleic Acids Res. 2015 Feb 27;43(4):e23. 3.
PMID: 25477383
PMCID: PMC4344483

Mayrhofer M, DiLorenzo S, Isaksson A "Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue" Genome Biol. 2013 Mar 25;14(3):R24. doi: 10.1186/gb-2013-14-3-r24
PMID: 23531354
PMCID: PMC4053982

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