This is a brief list of all file extensions generated by PLINK 2.0, along with content summaries and links to the associated flag(s). See the file formats appendix for detailed specifications.
| Extension | Source(s) | Contents |
| .*.<number> | --parallel | Partial result of distributed computation. |
| .acount | --freq counts | Allele count report (dosages considered). |
| .adjusted | --adjust, --adjust-file | Multiple-testing-corrected association analysis p-values. |
| .afreq | --freq | Allele frequency report (dosages considered). |
| .allele.no.snp | --update-alleles | Variants skipped due to mismatching old allele(s). |
| .bcf | --export bcf[-4.2] | Variant Call Format (v4.2 or 4.3), binary form. |
| .bed | --make-bed... | PLINK 1 binary biallelic genotype table. Could be sample-major. |
| .bgen | --export bgen... | Oxford variant information + genomic data binary file, v1.1-v1.3. |
| .bim | --make-bed... | PLINK 1 variant information file, part of binary fileset. |
| .bin | several | Matrix of binary floating point values. |
| .bins | --freq {ref,alt1}bins= | Allele count or frequency histogram. |
| .clumps | --clump | Reprocessed LD-clumped report. |
| .clumps.missing_allele | --clump | List of top (variant ID, A1) pairs skipped on account of A1. |
| .clumps.missing_id | --clump | List of top variant IDs missing from main dataset. |
| .cov | --write-covar... | Covariate table. |
| .eigenval | --pca | Principal component eigenvalues. |
| .eigenvec* | --pca | Principal component eigenvectors. |
| .fam | --make-bed... | PLINK 1 sample information text file, part of binary fileset. |
| .fst.summary | --fst | Between-population Wright's FST report. |
| .fst.var | --fst | Per-variant Wright's FST report for one population pair. |
| .gcount | --geno-counts | Genotype count report. |
| .gen | --export oxford | Oxford variant information + genomic data text file. |
| .glm.firth | --glm firth | Firth regression association statistics. |
| .glm.logistic | --glm no-firth | Logistic regression association statistics. |
| .glm.logistic.hybrid | --glm | Logistic/Firth hybrid regression association statistics. |
| .grm | --make-grm-list | GCTA relationship matrix (original format). |
| .grm.N.bin | --make-grm-bin | GCTA triangular binary observation count matrix. |
| .grm.bin | --make-grm-bin | GCTA triangular binary relationship matrix. |
| .*.gz | few | BGZipped file; use e.g. "gunzip <filename>" to unpack it. |
| .haps | --export haps... | Oxford phased haplotype file. |
| .hardy | --hardy | Hardy-Weinberg equilibrium exact test report (excludes chrX). |
| .hardy.x | --hardy | Graffelman-Weir chrX HWE exact test report. |
| .het | --het | Inbreeding coefficient report. |
| .*.id | lots | Ordered list of sample IDs associated with an analysis. |
| .kin0 | --make-king-table | KING-robust kinship coefficient report. |
| .king | --make-king | KING-robust kinship coefficient matrix. |
| .legend | --export hapslegend | Legend for Oxford .haps file with no header columns. |
| .map | --export ped | PLINK 1 text fileset variant information file. |
| .normalized | --normalize list | List of variants altered by --normalize. |
| .pdiff | --pgen-diff | Two-fileset genotype/dosage discordance report. |
| .ped | --export ped | PLINK 1 sample-major text pedigree + genotype file. |
| .pgen | --make-[b]pgen | PLINK 2 binary genomic data file. |
| .phy | --export phylip[-phased] | Relaxed PHYLIP multiple sequence alignment format. |
| .prune.in | --indep-pairwise | Pruned set of variants in approximate LD. |
| .prune.out | --indep-pairwise | IDs of variants excluded by LD-based prune. |
| .psam | --make-pgen... | PLINK 2 sample information file, part of binary fileset. |
| .pvar | --make-pgen... | PLINK 2 variant information file, part of binary fileset. |
| .raw | --export {A,AD} | Sample-major text dosage file. |
| .recoverid.dup | --recover-var-ids | List of current variant IDs with multiple possible original IDs. |
| .rel | --make-rel | Relationship or covariance matrix. |
| .rmdup.list | --rm-dup list | List of all duplicated variant IDs. |
| .rmdup.mismatch | --rm-dup | List of duplicate variant IDs with mismatched data. |
| .sample | --export | Oxford sample information text file. |
| .scount | --sample-counts | Sample variant-count report. |
| .sdiff | --sample-diff | Sample-pair discordance report. |
| .sdiff.summary | --sample-diff | Sample-pair discordance count summary. |
| .sexcheck | --{check,impute}-sex | Sex imputation report. |
| .smiss | --missing | Sample-based missing data report. |
| .snplist | --write-snplist | List of variant IDs surviving filters/inclusion thresholds. |
| .sscore | --score[-list] | Sample scores. |
| .ssf.tsv | --gwas-ssf | Association statistics in GWAS-SSF format. |
| .svd.pheno | --pheno-svd | Summary phenotypes generated via SVD. |
| .svd.pheno_wts | --pheno-svd | Singular values and right-singular vectors from phenotype SVD. |
| .tfam | --export tped | PLINK 1 sample information file, accompanied by .tped. |
| .tped | --export tped | PLINK 1 variant-major text variant information + genotype file. |
| .traw | --export Av | Variant-major text dosage file. |
| .used_sites.tsv | --export used-sites | Variant information for relaxed-PHYLIP file. |
| .vcf | --export vcf[-4.2] | 1000 Genomes Project Variant Call Format (v4.2 or 4.3). |
| .vcor | --r[2]-[un]phased | LD-statistic report. |
| .vcor1, .vcor2 | --r[2]-[un]phased | Variant-correlation matrix. |
| .vmiss | --missing | Variant-based missing data report. |
| .vscore | --variant-score | Text variant score report. |
| .vscore.bin | --variant-score | Binary variant score file. |
| .vscore.cols | --variant-score | Column headers (score names) accompanying .vscore.bin. |
| .vscore.vars | --variant-score | Variant IDs accompanying .vscore.bin. |
| .*.zst | pack | Zstd-compressed file; can be unpacked with --zst-decompress. |