Introduction, downloads

D: 20 Oct 2020

Recent version history

What's new?

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General usage

Getting started

Column set descriptors

Citation instructions

Standard data input

PLINK 1 binary (.bed)

PLINK 2 binary (.pgen)

Autoconversion behavior

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

Oxford genotype (.bgen)

Oxford haplotype (.haps)

PLINK 1 dosage

Sample ID conversion

Dosage import settings

Generate random

Unusual chromosome IDs

Allele frequencies

Phenotypes

Covariates

'Cluster' import

Reference genome (.fa)

Input filtering

Sample ID file

Variant ID file

Interval-BED file

--extract-col-cond

QUAL, FILTER, INFO

Chromosomes

SNPs only

Simple variant window

Multiple variant ranges

Deduplicate variants

Sample/variant thinning

Pheno./covar. condition

Missingness

Category subset

--keep-col-match

Missing genotypes

Number of distinct alleles

Allele frequencies/counts

Hardy-Weinberg

Imputation quality

Sex

Founder status

Main functions

Data management

--make-[b]pgen/--make-bed

--export

--output-chr

--split-par/--merge-par

--set-all-var-ids

--recover-var-ids

--update-map...

--update-ids...

--ref-allele

--ref-from-fa

--normalize

--indiv-sort

--write-covar

--variance-standardize

--quantile-normalize

--split-cat-pheno

--write-samples

Basic statistics

--freq

--geno-counts

--sample-counts

--missing

--genotyping-rate

--hardy

--het

--fst

--pgen-info

Linkage disequilibrium

--indep...

--ld

Sample comparison

Sample-distance matrices

Relationship/covariance

  (--make-grm-bin...)

--make-king...

--king-cutoff

Population stratification

--pca

PCA projection

Association analysis

--glm

--glm ERRCODE values

--adjust-file

Linear scoring

--score

--variant-score

Distributed computation

Command-line help

Miscellaneous

Flag/parameter reuse

System resource usage

--loop-cats

.zst decompression

Pseudorandom numbers

Warnings as errors

.pgen validation

Resources

1000 Genomes phase 3

Errors and warnings

Output file list

Order of operations

Google groups

Credits

File formats

Quick index search

Google groups

To be informed about updates, get technical support, make feature requests, and/or engage in other public communication about PLINK-related matters, you'll want to join one or two of our Google groups.

  • The plink2-announce group is the low-traffic choice, with nothing but major release announcements.
  • The plink2-users group is the general discussion and technical support forum. With luck, the archives will become useful over time as solutions to the most common issues accumulate. Release announcements will be crossposted here; we may also solicit feedback re: upcoming features.
  • plink2-dev 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 discuss it, 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.

To privately communicate with the development team (e.g. you have a potentially sensitive bug report), send email to wdist@cog-genomics.org.

Credits >>