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. 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.