Description

Compile a coverage reference from the given files (normal samples).

Input

name:type
description
pattern

fasta{:bash}

:file

File containing reference genome

*.{fasta}

targets{:bash}

:file

File containing genomic regions

*.{bed}

antitargets{:bash}

:file

File containing off-target genomic regions

*.{bed}

Output

name:type
description
pattern

cnn{:bash}

*.cnn{:bash}

:file

File containing a copy-number reference (required for CNV calling in tumor_only mode)

*.{cnn}

versions_cnvkit{:bash}

${task.process}{:bash}

:string

The name of the process

cnvkit{:bash}

:string

The name of the tool

cnvkit.py version | sed -e "s/cnvkit v//g"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

cnvkit{:bash}

:string

The name of the tool

cnvkit.py version | sed -e "s/cnvkit v//g"{:bash}

:eval

The expression to obtain the version of the tool

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
included in
sarek
maintainers
Github user adamrtalbot
Github user priesgo
Github user SusiJo
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