Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

cns{:bash}

:file

CNVKit CNS file.

*.cns

vcf{:bash}

:file

Germline VCF file for BAF.

*.vcf{,.gz}

Output

name:type
description
pattern

cns{:bash}

meta{:bash}

:map

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

*.cns{:bash}

:file

CNS file.

*.cns

versions{:bash}

versions.yml{:bash}

: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.

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