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).
Currently the workflow includes the following steps:
- Variant and Heteroplasmy Detection using mutserve
- Haplogroup Detection using HaploGrep
- Contamination Detection
- Graphical Report Creation
Haplocheck is already available in mitoverse. Please click here to run your first contamination check.