Description

Copy number variant detection from high-throughput sequencing data

Input

name:type
description
pattern

meta:map

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

]

cnr:file

CNR file

*.cnr

cns:file

CNS file [Optional]

*.cns

Output

name:type
description
pattern

tsv

meta:map

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

]

*.tsv:file

TSV file

*.tsv

cnn

meta:map

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

]

*.cnn:file

CNN file

*.cnn

versions

versions.yml:file

File containing software versions

versions.yml

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.