Repository is deprecated. Please go to http://github.com/genepi/haplocheck for the latest contamination check based on mtDNA!
This repository includes the workflow for detection of contamination based on mixtures of mtDNA haplotypes.
- Install Cloudgene with the following commands
mkdir cloudgene
cd cloudgene
curl -s install.cloudgene.io | bash
- Install the Haplochecker contamination workflow
./cloudgene gh mtdna/haplochecker@latest
3a) Start the local web service and run
./cloudgene server
Open your web browser and enter http://localhost:8082. Use admin and admin1978 to login.
3b) Run on the command line
./cloudgene run mtdna-haplochecker --input <bam-folder> --inType bam --output <results-folder>