Introduction, downloads

S: 11 Dec 2023 (b7.2)

D: 11 Dec 2023

Recent version history

What's new?

Future development


Note to testers

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General usage

Getting started

Citation instructions

Standard data input

PLINK 1 binary (.bed)

Autoconversion behavior

PLINK text (.ped, .tped...)

VCF (.vcf[.gz], .bcf)

Oxford (.gen[.gz], .bgen)

23andMe text

Generate random

Unusual chromosome IDs

Recombination map

Allele frequencies



Clusters of samples

Variant sets

Binary distance matrix

IBD report (.genome)

Input filtering

Sample ID file

Variant ID file

Positional ranges file

Cluster membership

Set membership



SNPs only

Simple variant window

Multiple variant ranges

Sample/variant thinning

Covariates (--filter)

Missing genotypes

Missing phenotypes

Minor allele frequencies


Mendel errors

Quality scores


Main functions

Data management

















Merge failures

VCF reference merge




Basic statistics









Linkage disequilibrium





Distance matrices






Distance-pheno. analysis





Population stratification





Association analysis

Basic case/control

  (--assoc, --model)

Stratified case/control

  (--mh, --mh2, --homog)

Quantitative trait

  (--assoc, --gxe)

Regression w/ covariates

  (--linear, --logistic)




Monte Carlo permutation

Set-based tests

REML additive heritability

Family-based association





Report postprocessing









Allelic scoring (--score)

R plugins (--R)

Secondary input

GCTA matrix (.grm.bin...)

Distributed computation

Command-line help


Tabs vs. spaces

Flag/parameter reuse

System resource usage

Pseudorandom numbers


1000 Genomes

Teaching materials

Gene range lists

Functional SNP attributes

Errors and warnings

Output file list

Order of operations

For developers

GitHub repository


Core algorithms

Partial sum lookup

Bit population count

Ternary dot product

Vertical population count

Exact statistical tests

Multithreaded gzip

Adding new functionality

Discussion forums




File formats

Quick index search

Secondary input

Some analyses are best performed on a different genomic data representation than the standard biallelic genotype call table. The following commands are used to load these alternative representations.

Copy number variation

--cfile <prefix>
--cnv-list <filename>

--cfile specifies the prefix for a .cnv + .fam + input fileset. (The file is technically never required—it is autogenerated when needed.) --cnv-list specifies the full name of just the .cnv file.

If loading is successful, a .cnv.indiv and a .cnv.summary file will be produced. If these are all you want, you do not need to include any other flags in the run.

--gfile <prefix>

(Not implemented yet.) This references a .gvar + .fam + .map fileset, for common copy number polymorphism analysis.

Relationship matrix

--grm-gz [prefix]
--grm-bin [prefix]

--grm-gz accepts a prefix (default 'plink') for a .grm.gz + fileset. Similarly, --grm-bin loads a .grm.bin + .grm.N.bin + fileset.

At present, only the --rel-cutoff and --unrelated-heritability flags can act on this input. With --rel-cutoff, only a file containing the pruned individual set is generated by default; if you also want the corresponding relationship matrix, add --make-grm-gz/--make-grm-bin.

Copy number analysis >>