Recodes plink bfiles into a new text fileset applying different modifiers
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bed
:file
PLINK binary biallelic genotype table file
*.{bed}
bim
PLINK extended MAP file
*.{bim}
fam
PLINK sample information file
*.{fam}
ped
*.ped
PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default “–recode” or by “–recode 12”.
*.{ped}
map
*.map
PLINK text fileset variant information file. Produced by the default “–recode” or by “–recode 12”.
*.{map}
txt
*.txt
Text file. Produced by “–recode 23”. Can only be used in a file with only one sample.
*.{txt}
raw
*.raw
Additive + dominant component file. Produced by “–recode AD” or “–recode A”.
*.{raw}
traw
*.traw
Variant-major additive component file. Produced by “–recode A-transpose”.
*.{traw}
beagledat
*.beagle.dat
BEAGLE file
*.{beagle.dat}
chrdat
*.chr-*.dat
chr file
*.{chr-*.dat}
chrmap
.*chr-*.map
chr map file
*.{chr-*.map}
geno
*.recode.geno.txt
BIMBAM genotype file. Produced by “–recode bimbam”.
*.{recode.geno.txt}
pheno
*.recode.pheno.txt
BIMBAM phenotype file. Produced by “–recode bimbam”.
*.{recode.pheno.txt}
pos
*.recode.pos.txt
BIMBAM variant position file. Produced by “–recode bimbam”.
*.{recode.pos.txt}
phase
*.recode.phase.inp
fastPHASE format. Produced by “–recode fastphase”.
*.{recode.phase.inp}
info
*.info
Haploview map file. Produced by “–recode HV”.
*.{info}
lgen
*.lgen
PLINK long-format genotype file. Produced by “–recode lgen”.
*.{lgen}
list
*.list
Genotype list file. Produced by “–recode list”.
*.{list}
gen
*.gen
Oxford genotype file format. Produced by “–recode oxford”.
*.{gen}
gengz
*.gen.gz
Compressed Oxford genotype file format
*.{gen.gz}
sample
*.sample
Oxford sample information file. Produced by “–recode oxford”.
*.{sample}
rlist
*.rlist
Rare genotype list file. Produced by “–recode rlist”.
*.{rlist}
strctin
*.strct_in
Structure-format file. Produced by “–recode structure”.
*.{strct_in}
tped
*.tped
Transposed text PED file. Produced by “–recode transpose”.
*.{tped}
tfam
*.tfam
Transposed text FAM file. Produced by “–recode transpose”.
*.{tfam}
vcf
*.vcf
Variant calling file (VCF). Produced by “–recode vcf”.
*.{vcf}
vcfgz
*.vcf.gz
Compressed variant calling file (VCF). Produced by “–recode vcf bgz”.
*.{vcf.gz}
versions_plink
${task.process}
:string
The name of the process
plink
The name of the tool
plink --version 2>&1 | sed 's/^PLINK v//;s/ .*//'
:eval
The expression to obtain the version of the tool
versions
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
