Haplocheck is a contamination detection tool using the mtDNA phylogeny. You can upload alignment files (BAM,CRAM) or variant files (vcf, vcf.gz) and receive a graphical and textual report which can be shared with collaborators.

We provide haplocheck as a standalone pipeline and as a cloud web service (via https://mitoverse.i-med.ac.at).

Haplocheck Workflow

Currently the workflow includes the following steps:

Haplocheck is already available in mitoverse. Please click here to run your first contamination check.