Description

Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file.

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Genome FASTA.

*.fasta

meta2{:bash}

:map

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

exclude_bed{:bash}

:file

Additional regions to exclude, in BED format. Can be used multiple times.

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 accessible 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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