Introduction, downloads

S: 22 Oct 2024 (b.7.7)

D: 22 Oct 2024

Recent version history

What's new?

Future development

Limitations

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

Phenotypes

Covariates

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

Attribute-based

Chromosomes

SNPs only

Simple variant window

Multiple variant ranges

Sample/variant thinning

Covariates (--filter)

Missing genotypes

Missing phenotypes

Minor allele frequencies

Hardy-Weinberg

Mendel errors

Quality scores

Relationships

Main functions

Data management

--make-bed

--recode

--output-chr

--zero-cluster

--split-x/--merge-x

--set-me-missing

--fill-missing-a2

--set-missing-var-ids

--update-map...

--update-ids...

--flip

--flip-scan

--keep-allele-order...

--indiv-sort

--write-covar...

--[b]merge...

Merge failures

VCF reference merge

--merge-list

--write-snplist

--list-duplicate-vars

Basic statistics

--freq[x]

--missing

--test-mishap

--hardy

--mendel

--het/--ibc

--check-sex/--impute-sex

--fst

Linkage disequilibrium

--indep...

--r/--r2

--show-tags

--blocks

Distance matrices

Identity-by-state/Hamming

  (--distance...)

Relationship/covariance

  (--make-grm-bin...)

--rel-cutoff

Distance-pheno. analysis

  (--ibs-test...)

Identity-by-descent

--genome

--homozyg...

Population stratification

--cluster

--pca

--mds-plot

--neighbour

Association analysis

Basic case/control

  (--assoc, --model)

Stratified case/control

  (--mh, --mh2, --homog)

Quantitative trait

  (--assoc, --gxe)

Regression w/ covariates

  (--linear, --logistic)

--dosage

--lasso

--test-missing

Monte Carlo permutation

Set-based tests

REML additive heritability

Family-based association

--tdt

--dfam

--qfam...

--tucc

Report postprocessing

--annotate

--clump

--gene-report

--meta-analysis

Epistasis

--fast-epistasis

--epistasis

--twolocus

Allelic scoring (--score)

R plugins (--R)

Secondary input

GCTA matrix (.grm.bin...)

Distributed computation

Command-line help

Miscellaneous

Tabs vs. spaces

Flag/parameter reuse

System resource usage

Pseudorandom numbers

Resources

1000 Genomes

Teaching materials

Gene range lists

Functional SNP attributes

Errors and warnings

Output file list

Order of operations

For developers

GitHub repository

Compilation

Core algorithms

Partial sum lookup

Bit population count

Ternary dot product

Vertical population count

Exact statistical tests

Multithreaded gzip

Adding new functionality

Discussion forums

plink2-users

Credits

File formats

Quick index search

Discussion forums

If you want to be informed about updates, get technical support, make feature requests, and/or engage in other public communication about PLINK-related matters:

  • The plink2-announce Google group is the low-traffic choice, with nothing but major release announcements.
  • The plink2-users Google group is the technical support forum for users. With luck, the archives will become useful over time as solutions to the most common issues accumulate. Release announcements are crossposted here.
  • The GitHub issues page is for those working with the source code. If you want to implement something new and/or perform a useful refactoring, this is a good place to open a discussion, especially if you want to see your work merged into the main codebase; we'll try to answer your questions in enough detail to enable you to finish your job.

Credits >>