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SummaryRecent major cancer genome sequencing studies have used whole-genome sequencing to detect various types of genomic variation. However, a number of these studies have continued to rely on SNP array information to provide additional results for copy number and loss-of-heterozygosity estimation and assessing tumour purity. OncoSNP-SEQ is a statistical model-based approach for inferring copy number profiles directly from high-coverage whole genome sequencing data that is able to account for unknown tumour purity and ploidy.AvailabilityMATLAB code is available at the following URL: https://sites.google.com/site/oncosnpseq/.

Original publication

DOI

10.1093/bioinformatics/btt416

Type

Journal article

Journal

Bioinformatics (Oxford, England)

Publication Date

10/2013

Volume

29

Pages

2482 - 2484

Addresses

Department of Mathematics, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.

Keywords

Humans, Neoplasms, Sequence Analysis, DNA, Genomics, Ploidies, Loss of Heterozygosity, Polymorphism, Single Nucleotide, Genome, Software Design, DNA Copy Number Variations