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