Recodes plink bfiles into a new text fileset applying different modifiers
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}
PLINK extended MAP file
*.{bim}
fam{:bash}
PLINK sample information file
*.{fam}
ped{:bash}
*.ped{:bash}
PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default “—recode” or by “—recode 12”.
*.{ped}
map{:bash}
*.map{:bash}
PLINK text fileset variant information file. Produced by the default “—recode” or by “—recode 12”.
*.{map}
txt{:bash}
*.txt{:bash}
Text file. Produced by “—recode 23”. Can only be used in a file with only one sample.
*.{txt}
raw{:bash}
*.raw{:bash}
Additive + dominant component file. Produced by “—recode AD” or “—recode A”.
*.{raw}
traw{:bash}
*.traw{:bash}
Variant-major additive component file. Produced by “—recode A-transpose”.
*.{traw}
beagledat{:bash}
*.beagle.dat{:bash}
BEAGLE file
*.{beagle.dat}
chrdat{:bash}
*.chr-*.dat{:bash}
chr file
*.{chr-*.dat}
chrmap{:bash}
.*chr-*.map{:bash}
chr map file
*.{chr-*.map}
geno{:bash}
*.recode.geno.txt{:bash}
BIMBAM genotype file. Produced by “—recode bimbam”.
*.{recode.geno.txt}
pheno{:bash}
*.recode.pheno.txt{:bash}
BIMBAM phenotype file. Produced by “—recode bimbam”.
*.{recode.pheno.txt}
pos{:bash}
*.recode.pos.txt{:bash}
BIMBAM variant position file. Produced by “—recode bimbam”.
*.{recode.pos.txt}
phase{:bash}
*.recode.phase.inp{:bash}
fastPHASE format. Produced by “—recode fastphase”.
*.{recode.phase.inp}
info{:bash}
*.info{:bash}
Haploview map file. Produced by “—recode HV”.
*.{info}
lgen{:bash}
*.lgen{:bash}
PLINK long-format genotype file. Produced by “—recode lgen”.
*.{lgen}
list{:bash}
*.list{:bash}
Genotype list file. Produced by “—recode list”.
*.{list}
gen{:bash}
*.gen{:bash}
Oxford genotype file format. Produced by “—recode oxford”.
*.{gen}
gengz{:bash}
*.gen.gz{:bash}
Compressed Oxford genotype file format
*.{gen.gz}
sample{:bash}
*.sample{:bash}
Oxford sample information file. Produced by “—recode oxford”.
*.{sample}
rlist{:bash}
*.rlist{:bash}
Rare genotype list file. Produced by “—recode rlist”.
*.{rlist}
strctin{:bash}
*.strct_in{:bash}
Structure-format file. Produced by “—recode structure”.
*.{strct_in}
tped{:bash}
*.tped{:bash}
Transposed text PED file. Produced by “—recode transpose”.
*.{tped}
tfam{:bash}
*.tfam{:bash}
Transposed text FAM file. Produced by “—recode transpose”.
*.{tfam}
vcf{:bash}
*.vcf{:bash}
Variant calling file (VCF). Produced by “—recode vcf”.
*.{vcf}
vcfgz{:bash}
*.vcf.gz{:bash}
Compressed variant calling file (VCF). Produced by “—recode vcf bgz”.
*.{vcf.gz}
versions_plink{:bash}
${task.process}{:bash}
:string
The name of the process
plink{:bash}
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
versions{:bash}
Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
