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General usage

Getting started

Flag usage summaries

Column set descriptors

Citation instructions

Standard data input

PLINK 1 binary (.bed)

PROVISIONAL_REF?

PLINK 2 binary (.pgen)

Autoconversion behavior

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

Oxford genotype (.bgen)

Oxford haplotype (.haps)

EIGENSOFT binary

BIMBAM Mean Genotype

23andMe text

PLINK 1 text (.ped, .tped)

PLINK 1 dosage

Sample ID conversion

Dosage import settings

Generate random

Unusual chromosome IDs

Recombination map

Allele frequencies

Phenotypes

Covariates

'Cluster' import

Variant sets

Reference genome (.fa)

Input filtering

Sample ID file

Variant ID file

Interval-BED file

Set membership

Attribute-based

--extract-col-cond

QUAL, FILTER, INFO

Chromosomes

SNPs only

Palindromic SNPs

Simple variant window

Multiple variant ranges

Deduplicate variants

Sample/variant thinning

Pheno./covar. condition

Missingness

Category subset

--keep-col-match

Missing genotypes

Same-indiv selection

Number of distinct alleles

Allele frequencies/counts

Hardy-Weinberg

Imputation quality

Mendel errors

Sex

Founder status

Relationships

Data management

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

--export

--output-chr

--zero-cluster

--split-par/--merge-par

--set-me-missing

--set-all-var-ids

--recover-var-ids

--update-map...

--update-ids...

--flip

--flip-scan

--ref-allele

--ref-from-fa

--normalize

--indiv-sort

--write-covar

--variance-standardize

--quantile-normalize

--split-cat-pheno

--pheno-svd

--pmerge[-list]

--write-samples

--info-to-cols

Basic statistics

--freq

--geno-counts

--sample-counts

--missing

--genotyping-rate

--test-mishap

--hardy

--mendel

--het

--check-sex/--impute-sex

--fst

--pgen-info

Pairwise diffs

--pgen-diff

--sample-diff

Linkage disequilibrium

--indep...

--r[2]-[un]phased

--ld

--ld-score

--show-tags

--blocks

Sample-distance matrices

Identity-by-state/Hamming

Relationship/covariance

--make-king...

--king-cutoff

Runs of homozygosity

Population stratification

--pca

PCA projection

--neighbour

Association analysis

--glm

--glm ERRCODE values

--gwas-ssf

--test-missing

--adjust-file

Monte Carlo permutation

Family-based association

--tucc

Report postprocessing

--clump

--gene-report

--meta-analysis

Epistasis

--epistasis-boost

--epistasis

--twolocus

Linear scoring

--score[-list]

--variant-score

Distributed computation

Command-line help

Bundled utilities

ldsc

mtag

vcf_subset

Miscellaneous

Flag/parameter reuse

System resource usage

--loop-cats

.zst decompression

Pseudorandom numbers

Warnings as errors

.pgen validation

Resources

1000 Genomes phase 3

HGDP-CEPH

FASTA files

Errors and warnings

Output file list

Order of operations

Developer information

GitHub root

Python library

R library

Compilation

Adding new functionality

Discussion forums

Credits

File formats

Setup

Rules of Thumb

Data Exploration 1 — HWE, Allele Frequency Spectrum

Linkage

Regressions

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