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{:bash}

:map

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

vcf{:bash}

:file

VCF file

*.{vcf.gz}

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

Raw report in txt format

*.{txt}

html{:bash}

meta{:bash}

:map

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

*.html{:bash}

:file

Haplocheck HTML report

*.{html}

versions{:bash}

versions.yml{:bash}

: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.

github.com/genepi/haplocheck 10.1101/gr.256545.119
included in
rarediseasevariantcatalogue
maintainer
Github user lmtani
get in touch
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