mtdna / haplochecker

Contamination detection workflow based on mtDNA

Repository is deprecated. Please go to http://github.com/genepi/haplocheck for the latest contamination check based on mtDNA!

Haplochecker - Detection of Contamination in mtDNA studies

This repository includes the workflow for detection of contamination based on mixtures of mtDNA haplotypes.

Run Haplochecker

1. Install Cloudgene with the following commands

mkdir cloudgene
cd cloudgene
curl -s install.cloudgene.io | bash

2. 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>