Description

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

Input

name:type
description
pattern

fasta:file

File containing reference genome

*.{fasta}

targets:file

File containing genomic regions

*.{bed}

antitargets:file

File containing off-target genomic regions

*.{bed}

Output

name:type
description
pattern

cnn

*.cnn:file

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

*.{cnn}

versions

versions.yml: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.