D: 2 Jul 2025

Main functions

  (--make-grm-bin...)

Tutorials

Data Exploration 2 — Genomic Structure

Relationship Matrix

Genome-Wide Assocation Analyses (GWAS)

Post-Hoc

Formatting Files

Variant IDs

Reference Alleles

Format for R

Shortcuts

Quick index search

Order of operations

• If --zst-decompress present, decompress file to stdout and QUIT
• Load additional commands from --script
• Apply --rerun
• If --help present, print requested help entries and QUIT
• If --version present, print version and QUIT
• Apply --silent
• Apply --out, start logging
• Define chromosome set (--chr-set, --cow...; human if unspecified)
• Parse remaining command line flags in lexicographic order
• Note chromosome filter (--chr, --not-chr, --autosome, --autosome-par)
• Handle nonstandard input:
• --adjust-file, --gwas-ssf standalone jobs
• If --pgen-info with no .pvar file provided, scan header, print basic info, and QUIT
• Convert VCF (--vcf), BCF (--bcf), Oxford dosage (--bgen, --data/--gen), Oxford haplotype (--haps), EIGENSOFT (--eigfile/--eiggeno), PLINK 1 text (--pedmap/--ped, --tfile/--tped), or PLINK 1 dosage (--import-dosage) data to PLINK 2 binary, then QUIT if no other commands
• Generate random dataset (--dummy)
• Merge filesets (--pmerge, --pmerge-list; --set-all-var-ids/--set-missing-var-ids applied to all inputs at the start if necessary)
• Read main sample-info file, if necessary:
• Check for duplicate sample IDs
• Read main variant-info file, if necessary:
• Exclude variants with multi-character allele codes (--snps-only)
• Apply #-of-distinct-alleles filters (--min-alleles, --max-alleles)
• Apply QUAL/FILTER/INFO variant filters (--var-min-qual, --var-filter, --extract-if-info, --exclude-if-info, --require-info, --require-no-info)
• Assign chromosome-and-position-based names to variants (--set-all-var-ids, --set-missing-var-ids)
• Split or merge pseudoautosomal region (--split-par, --merge-par, --merge-x)
• Read main genotype file's header (--[b]pfile, --bfile, or freshly autoconverted)
• Transpose PLINK 1 sample-major .bed, if necessary
• Validate genotype file (--validate), then QUIT if no other commands
• Print basic information about .pgen (--pgen-info), then QUIT if no other commands
• Apply "--make-founders first"
• Load/create additional phenotypes (--pheno, --within, --family)
• Ignore phenotypes (--not-pheno)
• Check for duplicate allele codes, if necessary
• Select single variant range by ID (--from, --to, --snp, --exclude-snp, --window, --from-bp...)
• Select multiple variant ranges by ID (--snps, --exclude-snps)
• Update variant information (--recover-var-ids, --update-map, --update-name)
• Update allele information (--update-alleles)
• Extract/exclude variants by ID list(s) or intervals (--extract, --exclude, --extract-intersect)
• Extract variants based on text column string/substring match or range condition (--extract-fcol)
• Deduplicate variants (--rm-dup)
• Filter variants by position (--from-bp, --to-bp, --extract bed0, ...)
• Recode alleles to 1234/ACGT (--allele1234, --alleleACGT)
• Random thinning of variant set (--thin, --thin-count)
• Update sample information (--update-ids, --update-parents, --update-sex)
• Keep/remove samples by ID or ID list(s) (--keep, --remove, --keep-fam, --remove-fam, --indv)
• Filter samples based on text column string match (--keep-fcol)
• Filter samples based on phenotype existence (--require-pheno)
• Filter based on sex and/or founder status (--keep-males...)
• Random thinning of sample set (--thin-indiv, --thin-indiv-count)
• Calculate per-sample genotyping rate, remove samples below threshold (--mind)
• Set founder status for samples with missing parent(s) (--make-founders)
• Load covariates (--covar)
• Ignore covariates (--not-covar)
• Filter samples based on covariate existence (--require-covar)
• Filter samples based on phenotype/covariate conditions (--keep-if, --remove-if, --keep-cats, ...)
• Report remaining sample/sex/founder counts
• Split categorical phenotypes/covariates (--split-cat-pheno)
• Quantile-normalize phenotypes/covariates (--quantile-normalize, --pheno-quantile-normalize, --covar-quantile-normalize)
• Variance-standardize phenotypes/covariates (--variance-standardize, --covar-variance-standardize)
• Generate low-rank approximation of input phenotype matrix (--pheno-svd)
• Loop over categories (--loop-cats)
• Write sample IDs (--write-samples), then QUIT (or advance to next --loop-cats category) if no other commands
• Main variant filters:
• Load allele frequencies (--read-freq)
• Calculate needed allele/genotype frequencies
• Report overall genotyping rate (--genotyping-rate)
• Write allele/genotype frequencies to file (--freq, --geno-counts), then QUIT if no other commands
• Generate missing data reports (--missing), then QUIT if no other commands
• Remove variants below genotyping rate threshold (--geno)
• Hardy-Weinberg equilibrium report and/or exact test (--hardy, --hwe), then QUIT if no other commands
• Apply minor allele frequency and count filters (--maf, --max-maf, --mac, --max-mac)
• Apply imputation-quality filter (--mach-r2-filter)
• Enforce minimum spacing (--bp-space)
• Report remaining variant count
• Report sample variant-counts by type (--sample-counts)
• Report sample-pair discordances (--sample-diff)
• Calculate kinship matrix, if necessary
• Perform kinship-based pruning of samples (--king-cutoff)
• Write kinship matrix/table to disk (--make-king, --make-king-table)
• Calculate variance-standardized relationship matrix, if necessary
• Write relationship matrix to disk (--make-rel, --make-grm-list, --make-grm-bin)
• Extract principal components (--pca)
• Write .snplist file (--write-snplist)
• Change REF/ALT alleles (--maj-ref, --ref-allele, --alt-allele, --alt1-allele, --ref-from-fa)
• Left-normalize alleles (--normalize)
• Write .cov file (--write-covar; also induced by --make-pgen, --export, and similar commands)
• Write PLINK 1 or 2 binary fileset, first updating chromosome information if necessary (--make-[b]pgen, --make-bed, --make-just-pvar, --make-just-psam, --make-just-bim, --make-just-fam, --update-chr)
• Export genotype data to other formats (--export)
• Compare two filesets (--pgen-diff)
• Perform LD-based pruning (--indep-pairwise)
• Display LD statistics for a single pair of variants (--ld)
• Write LD-statistic matrix/table to disk (--r[2]-[un]phased)
• F inbreeding coefficient report (--het)
• F_ST fixation index report (--fst)
• Apply linear scoring system(s) to each sample (--score, --score-list)
• Apply linear scoring system(s) to each variant (--variant-score)
• Multi-covariate association test (--glm)
• Reformat new association test results (--gwas-ssf)
• If --loop-cats, select next category and jump back to "Loop over categories" step, if any categories left
• Organize association reports into LD-based clumps (--clump)
• Definitely QUIT

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