Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

cnvs{:bash}

:file

_CNVs file generated by FREEC

*._CNVs

ratio{:bash}

:file

ratio file generated by FREEC

*.ratio.txt

Output

name:type
description
pattern

p_value_txt{:bash}

meta{:bash}

:map

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

*.p.value.txt{:bash}

:file

CNV file containing p_values for each call

*.p.value.txt

versions_controlfreec{:bash}

${task.process}{:bash}

:string

The name of the process

controlfreec{:bash}

:string

The name of the tool

echo 11.6b{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

controlfreec{:bash}

:string

The name of the tool

echo 11.6b{:bash}

:eval

The expression to obtain the version of the tool

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
included in
sarek
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub