Benchmarking somatic variant calling with long-read data on mitochondrial DNA

In this study, we deeply investigate somatic low-level variant calling for long-read data. First, we prepared a gold standard from NGS data of mitochondrial genomes by merging the results from three different variant callers. Subsequently, the TGS mixtures were prepared, base-called, trimmed, and additional quality control (QC) was performed. Finally, the performance of two variant callers designed for short-read data and one low-level variant specific for long-read data was compared. We also highlight the advantages of employing different mtDNA haplotypes as validation sets, with mean read lengths at 11kb