Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Genome FASTA.

*.fasta

meta2 (map)

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

]

exclude_bed (file)

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

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

File containing accessible regions.

*.{bed}

versions (file)

File containing software versions

versions.yml
maintainers
Github user adamrtalbot
Github user priesgo
get in touch
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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 https://github.com/etal/cnvkit 10.1371/journal.pcbi.1004873