CCLid (Cancer Cell Line identification) is designed as a toolkit to address the lack of a publicly available resource for genotype-based cell line authentication. We developed this resource to allow for genotype-matching of any given cancer cell line to the 1,204 unique cell lines found in the CCLE dataset, with support to include additional SNP array datasets. Using the B-allele frequencies (BAFs) for all SNPs found in common between the input data and reference datasets, this tool will allow for a genotype matching operation that trains and uses a logistic model to calculate the probability of the best cell line matches. This is followed by a measure of genetic drift between isogenic lines by look for segments of the genome that have significantly different BAF values. This zenodo dataset contains the (sample x probeset) BAF matrix for the CCLE dataset, as well as supporting datasets to allow mapping of SNP probesets and genotype correction between SNP array technologies (i.e. Affymetrix SNP 6.0 and Illumina HumanOmni 2.5M). This also contains all the metadata for cell line identities in CCLE, GDSC, and gCSI as well their corresponding cellosaurus unique identifies.