Description

Produce a pruned subset of markers that are in approximate linkage equilibrium with each other.

Input

name:type
description
pattern

meta{:bash}

:map

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

bed{:bash}

:file

PLINK binary biallelic genotype table file

*.{bed}

bim{:bash}

:file

PLINK extended MAP file

*.{bim}

fam{:bash}

:file

PLINK sample information file

*.{fam}

window_size{:bash}

:string

Window size in variant count or kilobase (if the ‘kb’ modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold.

variant_count{:bash}

:string

Variant count to shift the window at the end of each step.

variance_inflation_factor{:bash}

:string

Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed.

Output

name:type
description
pattern

prunein{:bash}

meta{:bash}

:map

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

*.prune.in{:bash}

:file

File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other

*.{prune.in}

pruneout{:bash}

meta{:bash}

:map

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

*.prune.out{:bash}

:file

File with IDs of excluded variants

*.{prune.out}

versions_plink{:bash}

${task.process}{:bash}

:string

The name of the process

plink{:bash}

:string

The name of the tool

plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'{: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

plink{:bash}

:string

The name of the tool

plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'{:bash}

:eval

The expression to obtain the version of the tool

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# https://www.cog-genomics.org/plink/1.9/dev
maintainer
Github user atrigila
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