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

bed:file

PLINK binary biallelic genotype table file

*.{bed}

bim:file

PLINK extended MAP file

*.{bim}

fam:file

PLINK sample information file

*.{fam}

meta2:map

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

] meta2 is associated to VCF file input

vcf:file

Variant calling file (vcf)

*.{vcf}

meta3:map

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

] meta3 is associated to BCF file input

bcf:file

PLINK variant information + sample ID + genotype call binary file

*.{bcf}

meta4:map

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

] meta4 is associated to phenotype file input

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

epi

meta:map

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

*.epi.cc:file

PLINK epistasis file

*.{epi.cc}

episummary

meta:map

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

*.epi.cc.summary:file

PLINK epistasis summary file

*.{epi.cc.summary}

log

meta:map

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

*.log:file

PLINK epistasis log file

*.{log}

nosex

meta:map

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

*.nosex:file

Ambiguous sex ID file

*.{nosex}

versions

versions.yml:file

File containing software versions

versions.yml

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
maintainer
Github user davidebag
get in touch
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