OncoSNP-SEQ is an analytical tool for characterising copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data. 

Project at a Glance:

OncoSNP-SEQ contains the following novel features:Loci classified into one of a number of copy number aberration states, each state describes a particular form of copy number alteration and LOH event. 
  • Ability to model both normal DNA contamination and intra-tumour heterogeneity jointly.
  • Estimates baseline haploid read level for polyploid samples.
  • Inference using Bayesian methods allowing uncertainty in estimates to be characterised.
Source codes and executables for OncoSNP-SEQ are freely available for academic and non-commercial use.

Recent Announcements

  • OncoSNP-SEQ 2.0 OncoSNP-SEQ 2.0 has now been released and can be obtained by following instructions on the Downloads section.The release corresponds to the version used in:Yau (2014) "Accounting ...
    Posted Jun 6, 2014, 3:24 AM by Christopher Yau
  • process_pileup.pl The usage information specified that the SNP file should be in BED format, however, both the illumina_hg19.txt SNP file and the the process_pileup.pl script supplied were ...
    Posted Mar 17, 2014, 7:55 AM by Christopher Yau
  • OncoSNP-SEQ v1.04 Updated to v1.04, features include:- Added support for normal-tumour pair analysis for Illumina and Complete Genomics.- Minor algorithmic tweaks to achieve 10-20% speed ups when using tumour ...
    Posted Jan 4, 2014, 3:59 AM by Christopher Yau
  • OncoSNP-SEQ Update v1.03 An update to the software has been uploaded. The package now includes:New versions of the Complete Genomics preprocessing scriptsAn updated file reader to read gzipped or zipped OncoSNP ...
    Posted Sep 17, 2013, 8:46 AM by Christopher Yau
  • CG Script for Standard Analysis Pipeline MasterVar files The attached Perl script can be used to generate OncoSNP-SEQ input data from normal and tumour CG data files that have been processed separately using CG's Standard Analysis ...
    Posted Sep 17, 2013, 1:44 AM by Christopher Yau
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