Description

Transform bait intervals into targets more suitable for CNVkit.

Input

name:type
description
pattern

meta{:bash}

:map

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

baits{:bash}

:file

BED or interval file listing the targeted regions.

*.{bed}

meta2{:bash}

:map

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

annotation{:bash}

:file

Use gene models from this file to assign names to the target regions.

*.{txt,bed,gff3,pil}

Output

name:type
description
pattern

bed{:bash}

meta{:bash}

:map

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

*.bed{:bash}

:file

File containing target regions

*.{bed}

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 https://github.com/etal/cnvkit 10.1371/journal.pcbi.1004873
maintainers
Github user adamrtalbot
Github user priesgo
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