Description

Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others.

Input

Name (Type)
Description
Pattern

meta (map)

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

]
meta is associated to the PLINK native file input

meta2 (map)

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

]
meta2 is associated to VCF file input

meta3 (map)

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

]
meta3 is associated to BCF file input

meta4 (map)

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

]
meta4 is associated to phenotype file input

bed (file)

PLINK binary biallelic genotype table file

*.{bed}

bim (file)

PLINK extended MAP file

*.{bim}

fam (file)

PLINK sample information file

*.{fam}

bcf (file)

PLINK variant information + sample ID + genotype call binary file

*.{bcf}

vcf (file)

Variant calling file (vcf)

*.{vcf}

phe (file)

PLINK file containing phenotype information. This phenotype information can be read from the third column with the —pheno option or from a specific column with the —pheno-name option.

*.{phe}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

versions (file)

File containing software versions

versions.yml

epi (file)

PLINK epistasis file

*.{epi.cc}

episummary (file)

PLINK epistasis summary file

*.{epi.cc.summary}

log (file)

PLINK epistasis log file

*.{log}

nosex (file)

Ambiguous sex ID file

*.{nosex}
maintainer
Github user davidebag
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

plink
GPL

Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

cog-genomics.org/plink cog-genomics.org/plink/1.9/data#recode https://www.cog-genomics.org/plink/1.9/dev