Description

Copy number variant detection from high-throughput sequencing data

Input

name:type
description
pattern

meta{:bash}

:map

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

cnr{:bash}

:file

CNR file

*.cnr

cns{:bash}

:file

CNS file [Optional]

*.cns

Output

name:type
description
pattern

tsv{:bash}

meta{:bash}

:map

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

*.tsv{:bash}

:file

TSV file

*.tsv

versions_cnvkit{:bash}

${task.process}{:bash}

:string

The name of the process

cnvkit{:bash}

:string

The name of the tool

cnvkit.py version | sed -e "s/cnvkit v//g"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

cnvkit{:bash}

:string

The name of the tool

cnvkit.py version | sed -e "s/cnvkit v//g"{:bash}

:eval

The expression to obtain the version of the tool

Tools

cnvkit
Apache-2.0

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

cnvkit.readthedocs.io/en/stable
included in
sarek
maintainers
Github user adamrtalbot
Github user marrip
Github user priesgo
get in touch
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