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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

ped (file)

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

*.{ped}

map (file)

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

*.{map}

txt (file)

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

*.{txt}

raw (file)

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

*.{raw}

traw (file)

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

*.{traw}

beagle-dat (file)

Single BEAGLE unphased genotype file. Produced by “—recode beagle” in ‘beagle-nomap’ mode.

*.{beagle.dat}

chr-dat (file)

BEAGLE unphased genotype and variant information files. Produced by “—recode beagle”.

*.{*.chr-*.dat}

chr-map (file)

BEAGLE variant information files. Produced by “—recode beagle”.

*.{*chr-*.map}

geno (file)

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

*.{recode.geno.txt}

pheno (file)

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

*.{recode.pheno.txt}

pos (file)

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

*.{recode.pos.txt}

phase (file)

fastPHASE format. Produced by “—recode fastphase”.

*.{recode.phase.inp}

info (file)

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

*.{info}

lgen (file)

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

*.{lgen}

list (file)

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

*.{list}

gen (file)

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

*.{gen}

genz (file)

Compressed Oxford genotype file format. Produced by “—recode oxford gen-gz”.

*.{genz}

sample (file)

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

*.{sample}

rlist (file)

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

*.{rlist}

strctin (file)

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

*.{strct_in}

tped (file)

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

*.{tped}

tfam (file)

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

*.{tfam}

vcf (file)

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

*.{vcf}

vcfgz (file)

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

*.{vcf.gz}
maintainer
Github user atrigila
get in touch
Ask a question on Slack Open an issue on GitHub

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