Description

Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number

Input

Name (Type)
Description
Pattern

meta (map)

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

]

cns (file)

CNVKit CNS file.

*.cns

vcf (file)

Germline VCF file for BAF.

*.vcf{,.gz}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

output (file)

File containing copy number information in new format.

*.{bed,vcf,cdt,jtv,seg,interval_count}
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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