RT Journal
A1 Weissensteiner, Hansi
A1 Forer, Lukas
A1 Fendt, Liane
A1 Kheirkhah, Azin
A1 Salas, Antonio
A1 Kronenberg, Florian
A1 Schoenherr, Sebastian
T1 Contamination detection in sequencing studies using the mitochondrial phylogeny
JF Genome Research 
JO Genome Research 
YR 2021 
FD February 01 
VO 31 
IS 2 
SP 309 
OP 316 
DO 10.1101/gr.256545.119 
UL http://genome.cshlp.org/content/31/2/309.abstract 
AB Within-species contamination is a major issue in sequencing studies, especially for mitochondrial studies. Contamination can be detected by analyzing the nuclear genome or by inspecting polymorphic sites in the mitochondrial genome (mtDNA). Existing methods using the nuclear genome are computationally expensive, and no appropriate tool for detecting sample contamination in large-scale mtDNA data sets is available. Here we present haplocheck, a tool that requires only the mtDNA to detect contamination in both targeted mitochondrial and whole-genome sequencing studies. Our in silico simulations and amplicon mixture experiments indicate that haplocheck detects mtDNA contamination accurately and is independent of the phylogenetic distance within a sample mixture. By applying haplocheck to The 1000 Genomes Project Consortium data, we further evaluate the application of haplocheck as a fast proxy tool for nDNA-based contamination detection using the mtDNA and identify the mitochondrial copy number within a mixture as a critical component for the overall accuracy. The haplocheck tool is available both as a command-line tool and as a cloud web service producing interactive reports that facilitates the navigation through the phylogeny of contaminated samples.