Description

Find copy number aberrations

Input

Name (Type)
Description
Pattern

meta (map)

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

]

npz (file)

An NPZ file created with WisecondorX convert

*.npz

meta2 (map)

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

]

reference (file)

A reference NPZ file created with WisecondorX newref

*.npz

meta3 (map)

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

]

blacklist (file)

OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small)

*.bed

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

aberrations_bed (file)

OPTIONAL - Output abberations in BED format. This gets created with the --bed option

*_aberrations.bed

bins_bed (file)

OPTIONAL - Output bins in BED format. This gets created with the --bed option

*_bins.bed

segments_bed (file)

OPTIONAL - Output segments in BED format. This gets created with the --bed option

*_segments.bed

chr_statistics (file)

OPTIONAL - Statistics per chromosome in TXT format. This gets created with the --bed option

*_chr_statistics.txt

chr_plots (list)

OPTIONAL - A list containing the CNV plots of each chromosome. This gets created with the --plot option

[!genome_wide]*.png

genome_plot (file)

OPTIONAL - A plot containing the CNV information of the whole genome

genome_wide.png
maintainer
Github user nvnieuwk
get in touch
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Tools

wisecondorx
Attribution-NonCommercial-ShareAlike CC BY-NC-SA

WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes

github.com/CenterForMedicalGeneticsGhent/WisecondorX 10.1093/nar/gky1263