Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

target_bed{:bash}

:file

BED file of target intervals

*.bed

meta2{:bash}

:map

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

fasta{:bash}

:file

FASTA reference sequence of the genome being used

*.fasta

genome{:bash}

:string

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

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

Annotated targets optimized for copy number calling

*.txt

bed{:bash}

meta{:bash}

:map

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

*.bed{:bash}

:file

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

*.bed

versions{:bash}

versions.yml{:bash}

: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.
maintainers
Github user aldosr
Github user lbeltrame
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