Description

Generate on and off-target intervals for PureCN from a list of targets

Input

Name (Type)
Description
Pattern

meta (map)

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

]

target_bed (file)

BED file of target intervals

*.bed

meta2 (map)

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

fasta (file)

FASTA reference sequence of the genome being used

*.fasta

genome (string)

Genome used for the BED file (e.g., “hg38”, “mm10”…)

Output

Name (Type)
Description
Pattern

meta (map)

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

]

txt (file)

Annotated targets optimized for copy number calling

*.txt

bed (file)

Modified and optimized targets exported as a BED file.
Generate the file using the —export command-line switch
IntervalFile.R.

*.bed

versions (file)

File containing software versions

versions.yml
authors
Github user aldosr Github user lbeltrame
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

purecn
Artistic-2.0

Copy number calling and SNV classification using targeted short read sequencing

args_id: $args
bioconductor.org/packages/release/bioc/html/PureCN https://github.com/lima1/PureCN 10.1186/s13029-016-0060-z.