Description

Recodes plink bfiles into a new text fileset applying different modifiers

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}

Output

name:type
description
pattern

ped

meta:map

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

]

*.ped:file

PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default “—recode” or by “—recode 12”.

*.{ped}

map

meta:map

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

]

*.map:file

PLINK text fileset variant information file. Produced by the default “—recode” or by “—recode 12”.

*.{map}

txt

meta:map

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

]

*.txt:file

Text file. Produced by “—recode 23”. Can only be used in a file with only one sample.

*.{txt}

raw

meta:map

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

]

*.raw:file

Additive + dominant component file. Produced by “—recode AD” or “—recode A”.

*.{raw}

traw

meta:map

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

]

*.traw:file

Variant-major additive component file. Produced by “—recode A-transpose”.

*.{traw}

beagledat

meta:map

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

]

*.beagle.dat:file

BEAGLE file

*.{beagle.dat}

chrdat

meta:map

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

]

*.chr-*.dat:file

chr file

*.{chr-*.dat}

chrmap

meta:map

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

]

.*chr-*.map:file

chr map file

*.{chr-*.map}

geno

meta:map

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

]

*.recode.geno.txt:file

BIMBAM genotype file. Produced by “—recode bimbam”.

*.{recode.geno.txt}

pheno

meta:map

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

]

*.recode.pheno.txt:file

BIMBAM phenotype file. Produced by “—recode bimbam”.

*.{recode.pheno.txt}

pos

meta:map

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

]

*.recode.pos.txt:file

BIMBAM variant position file. Produced by “—recode bimbam”.

*.{recode.pos.txt}

phase

meta:map

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

]

*.recode.phase.inp:file

fastPHASE format. Produced by “—recode fastphase”.

*.{recode.phase.inp}

info

meta:map

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

]

*.info:file

Haploview map file. Produced by “—recode HV”.

*.{info}

lgen

meta:map

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

]

*.lgen:file

PLINK long-format genotype file. Produced by “—recode lgen”.

*.{lgen}

list

meta:map

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

]

*.list:file

Genotype list file. Produced by “—recode list”.

*.{list}

gen

meta:map

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

]

*.gen:file

Oxford genotype file format. Produced by “—recode oxford”.

*.{gen}

gengz

meta:map

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

]

*.gen.gz:file

Compressed Oxford genotype file format

*.{gen.gz}

sample

meta:map

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

]

*.sample:file

Oxford sample information file. Produced by “—recode oxford”.

*.{sample}

rlist

meta:map

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

]

*.rlist:file

Rare genotype list file. Produced by “—recode rlist”.

*.{rlist}

strctin

meta:map

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

]

*.strct_in:file

Structure-format file. Produced by “—recode structure”.

*.{strct_in}

tped

meta:map

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

]

*.tped:file

Transposed text PED file. Produced by “—recode transpose”.

*.{tped}

tfam

meta:map

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

]

*.tfam:file

Transposed text FAM file. Produced by “—recode transpose”.

*.{tfam}

vcf

meta:map

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

]

*.vcf:file

Variant calling file (VCF). Produced by “—recode vcf”.

*.{vcf}

vcfgz

meta:map

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

]

*.vcf.gz:file

Compressed variant calling file (VCF). Produced by “—recode vcf bgz”.

*.{vcf.gz}

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.