modules/cnvkit_reference

Compile a coverage reference from the given files (normal samples).

cnvkitreferencecnvcopy number

https://github.com/nf-core/modules/[...]/modules/nf-core/cnvkit/reference

Description

Compile a coverage reference from the given files (normal samples).

Input

Name (Type)

Description

Pattern

`fasta` (file)

File containing reference genome

*.{fasta}

`targets` (file)

File containing genomic regions

*.{bed}

`antitargets` (file)

File containing off-target genomic regions

*.{bed}

Output

Name (Type)

Description

Pattern

`meta` (map)

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

]

`reference` (file)

File containing a copy-number reference (required for CNV calling in tumor_only mode)

*.{cnn}

`versions` (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 https://github.com/etal/cnvkit 10.1371/journal.pcbi.1004873

modules/cnvkit_reference

Description