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D: 22 Dec 2024

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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)

PLINK 1 text (.ped, .tped)

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

--pheno-svd

--pmerge[-list]

--write-samples

Basic statistics

--freq

--geno-counts

--sample-counts

--missing

--genotyping-rate

--hardy

--het

--check-sex/--impute-sex

--fst

--pgen-info

Pairwise diffs

--pgen-diff

--sample-diff

Linkage disequilibrium

--indep...

--r[2]-[un]phased

--ld

Sample-distance matrices

Relationship/covariance

  (--make-grm-bin...)

--make-king...

--king-cutoff

Population stratification

--pca

PCA projection

Association analysis

--glm

--glm ERRCODE values

--gwas-ssf

--adjust-file

Report postprocessing

--clump

Linear scoring

--score[-list]

--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

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

Tutorials

Setup

Rules of Thumb

Data Exploration 1 — HWE, Allele Frequency Spectrum

Data Exploration 2 — Genomic Structure

Linkage

Relationship Matrix

Genome-Wide Assocation Analyses (GWAS)

Regressions

Post-Hoc

Formatting Files

bcftools

Variant IDs

Reference Alleles

Format for R

Shortcuts

Quick index search

Tutorial Shortcuts

About

These are shortcuts for generating the tutorial files used across tutorials. Some of these require generated files from prior tutorials. The reused files from tutorials are listed under their tutorial subheadings.

Data Exploration 2A: Linkage

Reused files with prefix: ./data/processed/all_hg38_qcd

time plink2 \ --pfile 'vzs' ./data/raw/all_hg38 \ --make-pgen \ --autosome \ --snps-only \ --hwe 0.05 keep-fewhet \ --maf 0.05 \ --set-all-var-ids @:#\$r,\$a \ --out ./data/processed/all_hg38_qcd

Reused files with prefix: ./data/processed/all_hg38_qcd_LE1

Requires: (pfiles) ./data/processed/all_hg38_qcd (above)

1. time plink2 \ --pfile ./data/processed/all_hg38_qcd \ --indep-pairphase 100 0.8 \ --out ./results/qc/qc3/all_hg38_qcd

2.

time plink2 \ --pfile ./data/processed/all_hg38_qcd \ --make-pgen \ --extract ./results/qc/qc3/all_hg38_qcd.prune.in \ --out ./data/processed/all_hg38_qcd_LE1

Data Exploration 2B: Relationship Matrix

Reused files with prefix: ./data/processed/all_hg38_qcd_LE1_pca

Requires: (pfiles) ./data/processed/all_hg38_qcd_LE1

time plink2 \ --pfile ./data/processed/all_hg38_qcd_LE1 \ --freq counts \ --keep-founders \ --pca biallelic-var-wts \ --out ./results/qc/qc3/all_hg38_qcd_LE1_pca

GWAS 1: Regressions

Reused files with prefix: ./results/gwas/all_hg38_qcd_LE1_simgwas_quant1b

Requires:
(pfiles) ./data/processed/all_hg38_qcd_LE1
(pca files) ./data/processed/all_hg38_qcd_LE1_pca

time plink2 \ --pfile ./data/processed/all_hg38_qcd_LE1 \ --glm hide-covar --covar ./results/qc/qc3/all_hg38_qcd_LE1_pca.eigenvec \ --pheno ../misc/simgwas/simgwas_quant1.pheno \ --pfilter 1e-6 \ --out ./results/gwas/all_hg38_qcd_LE1_simgwas_quant1b

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