This is a brief list of all file extensions generated by PLINK 1.9, 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. |
| .adjusted | --adjust | Multiple-testing-corrected association analysis p-values. |
| .allele.no.snp | --update-alleles | Allele mismatch report. |
| .annot | --annotate | PLINK report with position/variant ID-based annotations. |
| .assoc | --assoc | 1df allelic chi-square C/C association analysis report. |
| .assoc.dosage | --dosage | Dosage association analysis report (could be C/C or QT). |
| .assoc.fisher | --assoc fisher[-midp] | Association analysis report using Fisher p-values. |
| .assoc.linear | --linear | Multi-covariate quant. trait association analysis report. |
| .assoc.logistic | --logistic | Multi-covariate case/control association analysis report. |
| .auto.R | --R | R plugin function results. |
| .beagle.dat | --recode beagle-nomap | BEAGLE multi-chromosome sample + genome data file. |
| .bed | --make-bed; --merge... | PLINK binary biallelic genotype table. |
| .bed.vmaj | (automatic) | Variant-major .bed file (when input .bed is sample-major) |
| .bim | --make-bed...; --merge... | PLINK variant information file, part of binary fileset. |
| .*.bin | several | Matrix of binary floating point values. |
| .blocks* | --blocks | Estimated haplotype blocks. |
| .chr-*.dat | --recode beagle | BEAGLE single-autosome sample + genome data file. |
| .chr-*.map | --recode beagle | BEAGLE single-autosome variant information file. |
| .clst | --write-cluster | Pruned cluster list. |
| .clumped* | --clump | Reprocessed LD-clumped report. |
| .cluster* | --cluster | Hierarchical clustering report. |
| .cmh | --mh/--bd | Cochran-Mantel-Haenszel 2x2xK test report. |
| .cmh2 | --mh2 | Cochran-Mantel-Haenszel IxJxK test report. |
| .cnv.overlap | --cnv-check-no-overlap | Overlapping CNV segment report. |
| .cnv.summary | --cfile | Per-variant CNV summary. |
| .cov | --write-covar... | Covariate table. |
| .debug.R | --R debug | Sequence of R commands --R would normally execute. |
| .dfam | --dfam | Sib-TDT association report. |
| .diff | --[b]merge | Merge conflict report from --merge-mode 6 or 7. |
| .dist | --distance | Tab-delimited allele count distance matrix. |
| .dupvar | --list-duplicate-vars | Duplicate-position-and-alleles variant report. |
| .eigenval | --pca | Principal component eigenvalues. |
| .eigenvec* | --pca | Principal component eigenvectors. |
| .epi.* | --[fast-]epistasis | Epistatic interaction scan reports. |
| .fam | --make-bed...; --merge... | PLINK sample information text file, part of binary fileset. |
| .flipscan* | --flip-scan | Case/control strand inconsistency report. |
| .frq | --freq | Basic allele frequency report. |
| .frq.cc | --freq case-control | Case/control phenotype-stratified allele frequency report. |
| .frq.count | --freq counts | Basic allele count report. |
| .frq.strat | --freq | Cluster-stratified allele frequency report. |
| .frqx | --freqx | PLINK 1.9 allele + heterozygote count report. |
| .fst | --fst | Fixation index report. |
| .gen | --recode oxford | Oxford variant information + genomic data text file. |
| .genome | --genome | Identity-by-descent report. |
| .gplink | --gplink | Reserved for gPLINK. (Currently a simple error indicator.) |
| .grm | --make-grm-gz | 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. |
| .grm.id | --make-grm-gz... | With --grm-gz + --rel-cutoff, a pruned set of sample IDs. |
| .*.gz | pack | Gzipped file; use e.g. "gunzip <filename>" to unpack it. |
| .het | --het | Method-of-moments F coefficient estimates. |
| .hh | (automatic) | List of het. haploid and nonmale Ychr genotypes. |
| .hom | --homozyg... | Run-of-homozygosity list. |
| .hom.indiv | --homozyg... | Sample-based runs-of-homozygosity report. |
| .hom.overlap* | --homozyg group... | Overlapping ROH pool report. |
| .hom.summary | --homozyg... | SNP-based runs-of-homozygosity report. |
| .homog | --homog | Chi-square partitioning odds ratio homogeneity report. |
| .hwe | --hardy | Hardy-Weinberg equilibrium exact test statistic report. |
| .ibc | --ibc | GCTA inbreeding coefficient report. |
| .*.id | lots | Ordered list of sample IDs associated with an analysis. |
| .imiss | --missing | Sample-based missing data report. |
| .indel | --list-23-indels | List of variants with 23andMe-style indel calls. |
| .info | --recode HV[-1chr] | Haploview variant information file. |
| .irem | --mind | IDs of samples excluded by --mind. |
| .lasso | --lasso | LASSO variant effect size estimates. |
| .ld | --r/--r2 | Inter-variant correlation table or matrix. |
| .ldset | --set-r2 | List of same-set marker pairs violating r2 threshold. |
| .lgen | --recode lgen[-ref] | PLINK long-format genomic data file. |
| .list | --recode list | Genotype list file. |
| .lmiss | --missing | Variant-based missing data report. |
| .map | --recode | PLINK text fileset variant information file. |
| .mdist | --distance, --ibs-matrix | Space- or tab-delimited distance proportion matrix. |
| .mdist.missing | --cluster missing | Space-delimited identity-by-missingness matrix. |
| .mds | --mds-plot | Haploview-friendly multidimensional scaling report. |
| .mds.eigvals | --mds-plot eigvals | Multidimensional scaling eigenvalues. |
| .*mendel | --mendel | Mendel error reports. |
| .meta | --meta-analysis | Meta-analysis. |
| .mibs | --distance, --ibs-matrix | Space- or tab-delimited IBS matrix. |
| .missing | --test-missing | Case/control nonrandom missingness test report. |
| .missing.hap | --test-mishap | Adjacent locus-based nonrandom missingness report. |
| .missnp | --bmerge, --merge-list | List of variants with more than two alleles. |
| .model | --model | 5-test association analysis report. |
| .mperm | --model... | Association analysis max(T) permutation test report. |
| .nearest | --neighbour | Nearest neighbor distance report. |
| .nopred | --score | List of (non-dosage) --score input file problems. |
| .nosex | (automatic) | List of samples with ambiguous sex codes. |
| .occur.dosage | --dosage occur | Dosage data variant occurrence report. |
| .out.dosage | --write-dosage | Merged dosage data. |
| .ped | --recode | PLINK/Merlin/Haploview text sample + genome data file. |
| .perm | --model... | Association analysis adaptive permutation test report. |
| .pphe | --make-perm-pheno | Permuted phenotypes. |
| .prob | --meta-analysis | Meta-analysis rejected variant list. |
| .profile | --score | Allelic scoring results. |
| .prune.in | --indep... | Pruned set of markers in approximate LD. |
| .prune.out | --indep... | IDs of variants excluded by LD-based prune. |
| .qassoc | --assoc | Quantitative phenotype association analysis report. |
| .qassoc.gxe | --gxe | Quantitative trait interaction report. |
| .qassoc.means | --assoc | Quantitative trait means and SDs stratified by genotype. |
| .qfam | --qfam... | Family-based quantitative trait association report. |
| .range.report | --gene-report | Reprocessed gene-based report. |
| .raw | --recode {A,AD} | Additive + dominant component file. |
| .recode.*.txt | --recode bimbam[-1chr] | BIMBAM genomic data fileset. |
| .recode.phase.inp | --recode fastphase[-1chr] | fastPHASE genomic data file. |
| .recode.strct_in | --recode structure | Structure genomic data file. |
| .ref | --recode lgen-ref | Reference allele list accompanying .lgen fileset. |
| .rel | --make-rel | Tab-delimited relationship or covariance matrix. |
| .rel.id | --make-rel, --rel-cutoff | With --rel-cutoff, a pruned set of unrelated sample IDs. |
| .rlist | --recode rlist | Rare genotype list file. |
| .sample | --recode oxford | Oxford sample information text file. |
| .set | --write-set | Variant set membership list file. |
| .set.[m]perm | --model... | Set association permutation test report. |
| .set.table | --set-table | Variant set membership table. |
| .sexcheck | --check-sex... | X chromosome-based sex validity report. |
| .simfreq | --simulate[-qt] | Realized simulated dataset parameters. |
| .skip.3allele | --biallelic-only | List of variant IDs filtered out due to 3+ alleles. |
| .snplist | --write-snplist | List of variant IDs surviving filters/inclusion thresholds. |
| .tags* | --show-tags | Tagging variant list/report. |
| .tdt | --tdt | Transmission disequilibrium test report. |
| .tdt.poo | --tdt poo | Parent-of-origin analysis. |
| .tfam | --recode transpose | PLINK sample information file, part of transposed fileset. |
| .tped | --recode transpose | PLINK transposed text genotype table. |
| .traw | --recode A-transpose | Variant-major additive component file. |
| .tucc.* | --tucc | Pseudo case/control file(set). |
| .twolocus | --twolocus | 4x4 joint genotype count table. |
| .var.ranges | --write-var-ranges | Equal-size variant ranges. |
| .vcf | --recode vcf... | 1000 Genomes Project Variant Call Format (v4.2). |