Description

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

Input

name:type
description
pattern

meta:map

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

]

bed:file

PLINK binary biallelic genotype table file

*.{bed}

bim:file

PLINK extended MAP file

*.{bim}

fam:file

PLINK sample information file

*.{fam}

window_size: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:string

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

variance_inflation_factor: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

meta:map

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

]

*.prune.in:file

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

*.{prune.in}

pruneout

meta:map

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

]

*.prune.out:file

File with IDs of excluded variants

*.{prune.out}

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# https://www.cog-genomics.org/plink/1.9/dev
maintainer
Github user atrigila
get in touch
Ask a question on Slack Open an issue on GitHub