Replication Data for: Evaluating the Performance of Tools Used to Call Minority Variants from Whole Genome Short-Read Data

Several minority variant callers have been developed to describe the minority variants sub-populations from whole genome sequence data. These tools differ based on bioinformatics and statistical approaches used to distinguish between real errors and relevant low-frequency variants. This project evaluated the diagnostic performance of four published minority variant callers and assessed overall concordance used to report minority variants from short-read sequenced data. An ART-Illumina read simulation tool was used to generate artificial short-read datasets of varying coverage based on a Respiratory Syncytial Virus (RSV) reference genome. The samples were spiked with nucleotide variants at predetermined positions and frequencies and thereafter called using FreeBayes, LoFreq, Vardict, and VarScan2. To identify the effect of the quality of data on concordance and performance of the callers we included datasets with error profiles.