Description

Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing
the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides
users a graphical report to investigate the contamination further. Internally, it uses the
Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

vcf (file)

VCF file

*.{vcf.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

txt (file)

Raw report in txt format

*.{txt}

html (file)

Haplocheck HTML report

*.{html}
included in
rarediseasevariantcatalogue
author
Github user lmtani
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Tools

haplocheck
MIT

Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content.

github.com/genepi/haplocheck10.1101/gr.256545.119