Details

Haplocheck is a contamination tool using the mtDNA phylogeny and has been integrated into the mitoverse mtDNA platform based on Cloudgene.

Run Haplocheck locally

Using Cloudgene, the complete workflow can also be executed locally. The final report is located outfolder/report.

    curl -s install.cloudgene.io | bash -s 2.0.0-rc9
    ./cloudgene install https://github.com/genepi/haplocheck/releases/download/v1.0.2/haplocheck.zip
    ./cloudgene run haplocheck@1.0.2 --files <input-files> --output <folder>  

Input File Formats

Haplocheck accepts BAM/CRAM files, vcf.gz as an input.

Output File Formats

Haplocheck genereates a text file including summary statistics for each sample and a contamination status. It also provides a graphical report which can shared with collaborators.

Documentation

Please click here to get the latest documentation.

Blog

Check out our blog regarding mtDNA topics.

Contact

Hansi Weissensteiner (@haansi) and Sebastian Schoenherr (@seppinho); Division of Genetic Epidemiology, Medical University of Innsbruck;

Installation

Command Line

cloudgene install https://github.com/genepi/haplocheck/releases/download/v1.0.4/haplocheck.zip

GUI

1. Login to Clougene and open the Admin Panel
2. Click on Applications / Install App from URL
3. The installation dialog appears. Please enter the following information:
   
   

   https://github.com/genepi/haplocheck/releases/download/v1.0.4/haplocheck.zip

4. A confirmation dialog appears and you can change permissions for the application

Main Contributors

Sebastian Schoenherr (@seppinho)

Hansi Weissensteiner

Lukas Forer (@lukfor)

Version

1.0.4

Website

https://mitoverse.i-med.ac.at

Source

https://github.com/genepi/haplocheck