Allele-Specific Copy Number Analysis of Tumors

Description

This repository provides the ASCAT R package that can be used to infer tumour purity, ploidy and allele-specific copy number profiles.

ASCAT is described in detail in: Allele-specific copy number analysis of tumors. Van Loo P et al. PNAS (2010).

This repository also contains the code underlying additional publication: Allele-specific multi-sample copy number segmentation. Ross EM, Haase K, Van Loo P & Markowetz F. Bioinformatics (2020).

Installation

devtools::install_github('VanLoo-lab/ascat/ASCAT')

Testing

We provide some scripts and input data in the ExampleData folder.

Output

After running the ascat.runAscat function: ascat.output$segments

GC correction script

We provide a method that creates a GC correction file in the gcProcessing folder.

Supported arrays without matched germline

Custom10k, IlluminaASA, IlluminaGSAv3, Illumina109k, IlluminaCytoSNP, IlluminaCytoSNP850k, Illumina610k, Illumina660k, Illumina700k, Illumina1M, Illumina2.5M, IlluminaOmni5, Affy10k, Affy100k, Affy250k_sty, Affy250k_nsp, AffyOncoScan, AffyCytoScanHD, AffySNP6, HumanCNV370quad, HumanCore12, HumanCoreExome24, HumanOmniExpress12 and IlluminaOmniExpressExome.

Misc

For more information about ASCAT and other projects of our group, please visit our website.