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).
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