Description

Fast 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

fepi (file)

PLINK fast-epistasis file

*.{epi.cc}

fepisummary (file)

PLINK fast-epistasis summary file

*.{epi.cc.summary}

flog (file)

PLINK fast-epistasis log file

*.{log}

fnosex (file)

Ambiguous sex ID file

*.{nosex}

Tools

plink
GPL

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