Contamination detection in mtDNA

Haplocheck detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content.

The main features of haplocheck are:

A fast tool to detect in-sample contaminaton by analyzing the mitochondrial content of sequencing data.
Works both on VCF and BAM input files.
It estimates contamination by detecting polymorphic sites in the mtDNA data and classifies them into mitochondrial haplogroups using haplogrep.
It can be used as a proxy tool to estimate the nDNA contamination levels. Our results show that a high concordance to the 1000G contamination levels (using Verifybamid2) can be achieved but can vary in samples showing large differences in the mtDNA copy number (e.g. due to tissue/cell type).

Team

Hansi Weissensteiner, Dr.techn.
Senior Scientist

+43 512 9003 70564
hansi.weissensteiner@i-med.ac.at

Sebastian Schönherr, Dr.techn.
Professor of Computational Genomics

+43 512 9003 70579
sebastian.schoenherr@i-med.ac.at

Lukas Forer, PhD
Assistant Professor of Genome Informatics

+43 512 9003 70562
lukas.forer@i-med.ac.at

Haplocheck is available as a graphical web-service or on GitHub for local usage.

Full documentation for haplocheck can be found here.

Weissensteiner H, Forer L, Fendt L, Kheirkhah A, Salas A, Kronenberg F, Schoenherr S: Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 31:309-316, 2021. PMID: 33452015 Journal Article