This dataset consists of the reference data files, metadata and processed results files for the paper "Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants," which investigates clonality in normal human dermal fibroblast cell populations in 32 cell lines from distinct donors, using bulk whole-exome sequencing and single-cell RNA-sequencing data. This dataset contains everything required to reproduce the results presented in the paper from processed data and results of our data processing workflows. Our analyses can be reproduced using the source code and instructions available at our project website. The entire analysis workflow from raw data to final results is also reproducible but is substantially more complicated and computationally intensive. It also requires large datasets to be obtained from other repositories. Specifically, single-cell RNA-seq data have been deposited in the ArrayExpress database at EMBL-EBI under accession number E-MTAB-7167. Whole-exome sequencing data is available through the HipSci portal (www.hipsci.org). Combined with the dataset in this repository and following the instructions on the project website, it is possible to run our entire analysis pipeline.