CNAqc

CNAqc is a package to quality control (QC) bulk cancer sequencing data. Methods are available to , visualise and manipulate i) somatic mutation data of both single-nucleotide variants and insertion-deletions, ii) allele-specific Copy Number Alterations (CNAs) and iii) tumour purity estimates. QC procedures in CNAqc can be used to validate copy number segmentations against variant allele frequencies of somatic mutations; QC scores can be used to rank alternative tumour segmentations and purity/ ploidy estimates. The tool also provides an automatic copy number calling pipeline that uses the Sequenza caller algorithm. CNAqc provides also algorithms to phase mutation multiplicities against CNAs and estimate Cancer Cell Fractions (CCFs) with their uncertainty. The package contains also statistical tests to identify patterns of over-fragmentation of chromosome arms (excessively short and numerous DNA fragments) and perform various manipulation tasks for somatic tumour data.

Citation

If you use CNAqc, please cite:

• Integrated quality control of allele-specific copy numbers, mutations and tumour purity from cancer whole genome sequencing assays Jacob Househam, Riccardo Bergamin, Salvatore Milite, Nicola Calonaci, Alice Antonello, Marc J Williams, William CH Cross, Giulio Caravagna. biorXiv 2022.

Help and support

Installation

# install.packages("devtools")
devtools::install_github("caravagnalab/CNAqc")

Copyright and contacts

Cancer Data Science (CDS) Laboratory, University of Trieste, Italy.