Introduction, downloads

S: 11 Dec 2023 (b7.2)

D: 11 Dec 2023

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

Google groups

plink2-users

plink2-dev

Credits

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 + .cnv.map input fileset. (The .cnv.map 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 + .grm.id fileset. Similarly, --grm-bin loads a .grm.bin + .grm.N.bin + .grm.id fileset.

At present, only the --rel-cutoff and --unrelated-heritability flags can act on this input. With --rel-cutoff, only a .grm.id 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 >>