Haplocheck: Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies

There are many examples in the literature showing the negative impact of within-species contamination in sequencing datasets. Here, we describe haplocheck, a software tool that uses the human mitochondrial phylogeny to estimate the contamination level within samples. By analyzing wet-lab and in-silico mixtures, we show that haplocheck is able to detect contamination accurately in mitochondrial sequencing studies. We further demonstrate that haplocheck can be used as an efficient proxy for estimating the nuclear DNA contamination level and investigate the influence of the mitochondrial copy number. Haplocheck is available at .