Description

Copy number variant detection from high-throughput sequencing data

Input

name:type
description
pattern

meta{:bash}

:map

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

tumor{:bash}

:file

Input tumour sample bam file (or cram)

normal{:bash}

:file

Input normal sample bam file (or cram)

meta2{:bash}

:map

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

fasta{:bash}

:file

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

meta3{:bash}

:map

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

fasta_fai{:bash}

:file

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

meta4{:bash}

:map

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

targets{:bash}

:file

Input target bed file

meta5{:bash}

:map

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

reference{:bash}

:file

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

panel_of_normals{:bash}

:file

Input panel of normals file

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 genomic regions

*.{bed}

cnn{:bash}

meta{:bash}

:map

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

*.cnn{:bash}

:file

File containing coverage information

*.{cnn}

cnr{:bash}

meta{:bash}

:map

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

*.cnr{:bash}

:file

File containing copy number ratio information

*.{cnr}

cns{:bash}

meta{:bash}

:map

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

*.cns{:bash}

:file

File containing copy number segment information

*.{cns}

pdf{:bash}

meta{:bash}

:map

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

*.pdf{:bash}

:file

File with plot of copy numbers or segments on chromosomes

*.{pdf}

png{:bash}

meta{:bash}

:map

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

*.png{:bash}

:file

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

*.{png}

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
included in
createpanelrefssarek
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