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:false ]

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

txt

meta:map

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

*.txt:file

Annotated targets optimized for copy number calling

*.txt

bed

meta:map

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

*.bed:file

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

*.bed

versions

versions.yml:file

File containing software versions

versions.yml

Tools

purecn
Artistic-2.0

Copy number calling and SNV classification using targeted short read sequencing

bioconductor.org/packages/release/bioc/html/PureCN https://github.com/lima1/PureCN 10.1186/s13029-016-0060-z.
Github user aldosr
Github user lbeltrame
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