Welcome to Haplocheck!

Haplocheck is a contamination detection tool using the mtDNA phylogeny. Haplochecks only requires the mitochondrial genome as an input to detect contamination in both mtDNA and whole-genome sequencing studies. It can therefore be used as a proxy for a quick contamination check.

You can upload alignment files (BAM,CRAM) or variant files (vcf format) 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.