Description

Copy number variant detection from high-throughput sequencing data

Input

Name (Type)
Description
Pattern

meta (map)

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

]

tumor (file)

Input tumour sample bam file (or cram)

normal (file)

Input normal sample bam file (or cram)

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

fasta (file)

Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

fasta_fai (file)

Input reference genome fasta index (optional, but recommended for cram_input)

meta4 (map)

Groovy Map containing information about target file
e.g. [ id:‘test’ ]

targets (file)

Input target bed file

meta5 (map)

Groovy Map containing information about reference file
e.g. [ id:‘test’ ]

reference (file)

Input reference cnn-file (only for germline and tumor-only running)

panel_of_normals (file)

Input panel of normals file

Output

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

File containing genomic regions

*.{bed}

cnn (file)

File containing coverage information

*.{cnn}

cnr (file)

File containing copy number ratio information

*.{cnr}

cns (file)

File containing copy number segment information

*.{cns}

pdf (file)

File with plot of copy numbers or segments on chromosomes

*.{pdf}

png (file)

File with plot of bin-level log2 coverages and segmentation calls

*.{png}

versions (file)

File containing software versions

versions.yml
included in
createpanelrefs sarek
maintainers
Github user adamrtalbot
Github user drpatelh
Github user fbdtemme
Github user kaurravneet4123
Github user KevinMenden
Github user lassefolkersen
Github user MaxUlysse
Github user priesgo
Github user SusiJo
get in touch
Ask a question on Slack Open an issue on GitHub

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