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

]

vcf:file

VCF file

*.{vcf.gz}

Output

name:type
description
pattern

txt

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.txt:file

Raw report in txt format

*.{txt}

html

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.html:file

Haplocheck HTML report

*.{html}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

haplocheck
MIT

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