Description

Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC

Input

Name (Type)
Description
Pattern

meta (map)

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

]

cnvs (file)

_CNVs file generated by FREEC

*._CNVs

ratio (file)

ratio file generated by FREEC

*.ratio.txt

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

p_value_txt (file)

CNV file containing p_values for each call

*.p.value.txt
included in
sarek
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

controlfreec/assesssignificance
GPL >=2

Copy number and genotype annotation from whole genome and whole exome sequencing data.

http://boevalab.inf.ethz.ch/FREEC http://boevalab.inf.ethz.ch/FREEC/tutorial https://github.com/BoevaLab/FREEC/ 10.1093/bioinformatics/btq635