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{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
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