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OncoSNP-SEQ specifications


Unique identifier OMICS_00348
Name OncoSNP-SEQ
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Version 2.01
Stability Stable
Maintained Yes




No version available



  • person_outline Christopher Yau

Additional information


Publication for OncoSNP-SEQ

OncoSNP-SEQ citations


Engineered in vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer

Sci Rep
PMCID: 5647443
PMID: 29044127
DOI: 10.1038/s41598-017-13338-8

[…] Copy number information for Experiment 2 was obtained from OncoSNP-SEQ analysis of the DAH55 and DAH56 cell line copy number array measurements (SNP6). […]


Whole genome sequencing of spermatocytic tumors provides insights into the mutational processes operating in the male germline

PLoS One
PMCID: 5439955
PMID: 28542371
DOI: 10.1371/journal.pone.0178169

[…] ual inspection of both read depth ratio and BAF was initially used to infer the whole-chromosome alterations. These large-scale copy number alterations and loss of heterozygosity were confirmed using OncoSNP-SEQ [], a statistical model-based approach for inferring copy number profiles directly from high-coverage whole-genome sequencing data. To reduce false positives, only OncoSNP-SEQ calls obtain […]


Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates

PMCID: 4765721
PMID: 26962434
DOI: 10.5256/f1000research.8030.r11450

[…] mber profile and clonality. These include e.g. ABSOLUTE ( www.broadinstitute.org/cancer/cga/absolute) , ASCAT ( heim.ifi.uio.no/bioinf/Projects/ASCAT) , CloneHD ( github.com/andrej-fischer/cloneHD) , OncoSNP-SEQ ( sites.google.com/site/oncosnpseq/) and QPure ( sourceforge.net/projects/qpure/) (for a more complete review see Yadav and De. ). There are real problems of model identifiability in per […]


Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

Nat Genet
PMCID: 4601524
PMID: 25985138
DOI: 10.1038/ng.3304

[…] along the chromosome. This procedure served to remove noise in the data due to biases in sequence composition. Candidate CNVs (down to about 10 kb) were identified as outliers visually. 2) We applied OncoSNP-SEQ in germline mode to a subset of 300,000 reliable SNPs across the genome. Coverage and read counts at these locations were used as proxy for the intensity and B-allelic-frequency under a sp […]


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OncoSNP-SEQ institution(s)
Department of Mathematics, South Kensington Campus, Imperial College London, London, UK

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