PLINK: Whole genome data analysis toolset plink...
Last original PLINK release is v1.07 (10-Oct-2009); PLINK 1.9 is now available for beta-testing

Whole genome association analysis toolset

Introduction | Basics | Download | Reference | Formats | Data management | Summary stats | Filters | Stratification | IBS/IBD | Association | Family-based | Permutation | LD calcualtions | Haplotypes | Conditional tests | Proxy association | Imputation | Dosage data | Meta-analysis | Result annotation | Clumping | Gene Report | Epistasis | Rare CNVs | Common CNPs | R-plugins | SNP annotation | Simulation | Profiles | ID helper | Resources | Flow chart | Misc. | FAQ | gPLINK

1. Introduction

2. Basic information

3. Download and general notes

4. Command reference table

5. Basic usage/data formats 6. Data management

7. Summary stats 8. Inclusion thresholds 9. Population stratification 10. IBS/IBD estimation 11. Association 12. Family-based association 13. Permutation procedures 14. LD calculations 15. Multimarker tests 16. Conditional haplotype tests 17. Proxy association 18. Imputation (beta) 19. Dosage data 20. Meta-analysis 21. Annotation 22. LD-based results clumping 23. Gene-based report 24. Epistasis 25. Rare CNVs 26. Common CNPs 27. R-plugins 28. Annotation web-lookup 29. Simulation tools 30. Profile scoring 31. ID helper 32. Resources 33. Flow-chart 34. Miscellaneous 35. FAQ & Hints

36. gPLINK
 

This page is not currently completely up-to-date as of v1.07, although the majority of commands and output files are listed.

Options

Option Parameter/default Description
Basic input/output
--file {plink} Specify .ped and .map files
--ped {plink.ped} Specify .ped file
--map {plink.map} Specify .map file
--no-sex PED file does not contain column 5 (sex)
--no-parents PED file does not contain columns 3,4 (parents)
--no-fid PED file does not contain column 1 (family ID)
--no-pheno PED file does not contain column 6 (phenotype)
--liability PED file does contain liability (column 7)
--map3 Specify 3-column MAP file format
     
--tfile {plink} Specify .tped and .tfam files
--tped {plink.tped} Specify .tped file
--tfam {plink.tfam} Specify .tfam file
     
--lfile {plink} Specify long-format: LGEN, FAM and MAP
     
--bfile {plink} Specify .bed, .bim and .fam
--bed {plink.bed} Specify .bed file
--bim {plink.bim} Specify .bim file
--fam {plink.fam} Specify .fam file
     
--out {plink} Specify output root filename
--silent Suppress output to console
     
--pheno {phenofile} Specify alternate phenotype
--make-pheno {file} {value} Specify binary phenotype, with cases have value
--make-pheno {file} * Specify binary phenotype, with cases are present
--mpheno {var #} Specify which, if >1 phenotype column
--pheno-name {var name} Instead of --mpheno, if a header row exists
--all-pheno Perform association for all phenotypes in file
--loop-assoc {clusterfile} Perform association for each level of cluster versis all others
     
--covar {covarfile} Specify covariate
--mcovar {var #} Specify which, if >1 covariate column (for use with --gxe)
--covar-name {list} Specify 1 or more covariates by name
--covar-number {list} Specify 1 or more covariates by number
     
--within {filename} Specify clustering scheme
--mwithin {var #} Specify which, if >1 cluster column
     
--script {filename} Include command-line options from file
     
Selection of SNPs and individuals
--chr {N} Select a particular chromosome N
--gene {name} Select a particular gene, given a SET file (--set)
     
--from {SNP} Select range from this SNP ...
--to {SNP} ... to this SNP (must be on same chromosome)
     
--snps {SNP list} Select comma-delimited list of SNPs, allowing for ranges, e.g. snp1,snp2,snp6-snp12
     
--snp {SNP} Select this SNP ...
--window {kb} ... and (optionally) all SNPs in the surrounding kb window
     
--from-bp {bp} Select SNPs within this window...
--to-bp {bp} ... specified in base-pair position
     
--from-kb {kb} Select SNPs within this window...
--to-kb {kb} ... specified in kilobases
     
--from-mb {mb} Select SNPs within this window...
--to-mb {mb} ... specified in megabases
     
--extract {snplist} Extract list of SNPs
--exclude {snplist} Exclude list of SNPs
     
--keep {indlist} Keep only these individuals
--remove {indlist} Remove these individuals
     
--keep-before-remove Perform keep before remove (default opposite)
--exclude-before-extract Perform exclude before extract (default opposite)
     
--filter {filename} {value} Filter individuals matching value
--mfilter {var #} Specify filter value, if >1 filter column
     
--filter-cases Include only cases
--filter-controls Include only controls
--filter-males Include only males
--filter-females Include only females
--filter-founders Include only founders
--filter-nonfounders Include only nonfounders
--prune Remove individuals with missing phenotypes
     
Other data management options
--make-bed Make .bed, .fam and .bim
--recode Output new .ped and .map files
--recode12 As above, with 1/2 allele coding
--recode-rlist List individuals with minor allele genotypes
--recode-lgen Output data in long LGEN format
     
--recodeHV As above, with Haploview .info file
--recode-fastphase Ouput fastphase format file
--recode-bimbam Ouput bimbam format file
--recode-structure Ouput structure format file
     
--recodeA Raw data file with additive coding
--recodeAD Raw data file with additive/dominance coding
--tab Delimit --recode and --recode12 with tabs
--list Output one genotype per line, list of FIDs and IIDs
--plist {FID1 IID1 FID2 IID2} Pairwise listing of genotypes for two individuals
     
--write-snplist List only the (filtered) SNPs in the dataset
--update-map {filename} Update physical positions in a map file
--update-cm Update genetic distances in a map file
--update-name Update SNP names in a map file
--update-chr Update chromosome codes in a map file
     
--update-ids {file} Update FIDs and IIDs in a file
--update-sex {file} Update sex information in a file
--update-parents {file} Update parent codes in a file
     
--write-covar Output ordered, filtered covariate file
--with-phenotype Include PED/phenotype information in new covariate file
--dummy-coding Downcode categorical covariates to binary dummy variables
     
--merge {pedfile}, {mapfile} Merge in a PED/MAP fileset
--bmerge {bedfile}, {bimfile}, {famfile} Merge in a binary fileset
--merge-list {list file} Merge multiple standard and/or binary filesets
--merge-mode {1} Specify merge mode (1-7)
     
--zero-cluster {filename} Zero-out specific SNPs for specific clusters
--oblig-missing {filename} SNPs/clusters that are obligatory missing
--oblig-cluster {filename} Individuals/clusters defining obligatory missingness
     
--flip {snplist} Flip strand of SNPs in list
--flip-subset {individual-list} Flip strand of SNPs only for these individuals in list
--flip-scan LD-based heuristic to look for SNPs flipped between cases and controls
     
--1 0/1 unaffected/affected coding
--compound-genotypes Use AA, AG, 00 coding (no spaces between alleles in PED file)
--missing-phenotype {-9} Missing phenotype code
--missing-genotype {0} Missing genotype code
--output-missing-phenotype {-9} Missing phenotype code for output
--output-missing-genotype {0} Missing genotype code for output
--allele1234 Convert (A,C,G,T) to (1,2,3,4)
--alleleACGT Convert (1,2,3,4) to (A,C,G,T)
--update-alleles {file} Update allele codes in a file
--reference-allele {file} Force a particular reference (A1) allele
--keep-allele-order Do not flip A1 to be the minor allele
     
--allow-no-sex Do not set ambiguously-sexed individuals missing
--must-have-sex When making a new dataset, do set ambiguously-sexed individuals missing
--set-hh-missing Making new fileset, set heterozygous haploids missing
--set-me-missing Making new fileset, set Mendel errors missing
     
--make-founders Set non-founders without two parents to founders
--pedigree When performing TDT, dump parsed family structure
--tucc Make pseudo case/control pairs form trio data
     
Reporting summary statistics
--freq Allele frequencies
--counts Modifies --freq to report actual allele counts
--nonfounders Include all individuals in MAF/HWE calculations
     
--missing Missing rates (per individual, per SNP)
--test-missing Test of missingness differing by case/control status
--test-mishap Haplotype-based test for non-random missingness
--cluster-missing IBM clustering
     
--hardy Report Hardy-Weinberg disequilibrium tests (exact)
--hardy2 Report Hardy-Weinberg disequilibrium tests (asymptotic)
--mendel Report Mendel error checks
     
--check-sex Use X chromosome data to check an individual's assigned sex
--impute-sex Use X chromosome data to impute an individual's assigned sex
     
--within {cluster file} Stratify frequencies and missing rates by clusters
     
Inclusion thresholds
--maf {0.01} Minor allele frequency
--max-maf {1} Maximum minor allele frequency
--geno {0.1} Maximum per-SNP missing
--mind {0.1} Maximum per-person missing
--hwe {0.001} Hardy-Weinberg disequilibrium p-value (exact)
--hwe2 {0.001} Hardy-Weinberg disequilibrium p-value (asymptotic)
--hwe-all HW filtering based on all founder individuals for binary trait (instead of just unaffecteds)
--me {0.1} {0.1} Mendel error rate thresholds (per SNP, per family)
--cell {5} Minimum genotype cell count for --model
--min {0} Minimum pi-hat for --genome output
--max {1} Maximum pi-hat for --genome output
     
Quality scores
--qual-scores {file} SNP based quality scores filter
--qual-threshold {0.8} SNP quality score threshold
--qual-max-threshold {1} SNP maximum quality scores threshold
--qual-geno-scores {file} Genotype-based quality scores filter
--qual-geno-threshold {0.8} Genotype quality score threshold
--qual-geno-max-threshold {1} Genotype maximum quality scores threshold
     
IBS stratification / clustering
--genome Calculate IBS distances between all individuals
--cluster Perform clustering
--matrix Output IBS (similarity) matrix
--distance-matrix Output 1-IBS (distance) matrix
--mc {0} Maximum cluster size
--cc Cluster by phenotype
--mcc {0 0} Maximum number of cases/controls per cluster
--ibm {0.01} Constrain IBS matching on IBM matching
--ppc {0.01} IBS test p-value threshold (was --pmerge)
--ppc-gap {500kb} Skip SNPs within this for PPC test
--match {match-file} Specify external categorical matching criteria
--match-type {match-type-file} Specify external categorical matching direction (+/- match)
--qmatch {match-file} Specify external quantitative matching criteria
--qt {threshold-file} Specify quantitative matching thresholds
--neighbour {N} {M} Outlier statistics (for nearest neighbours N to M)
     
Whole genome summary statistics
--genome Output genome-wide IBS/IBD
--rel-check Only calculate IBS/IBD for members of same family (FID)
--read-genome {genome-file} Read previously-computed genome values
--nudge Adjusted estimated IBD values
--impossible Indicate 'impossible' estimated IBD values
--het Individual inbreeding F / heterozygosity
--homozyg-kb {kb} Identify runs of homozygosity (kb)
--homozyg-snp {N SNPs} Identify runs of homozygosity (# SNPs)
--homozyg-het {N hets} Allow for N hets in run of homozygosity
--homozyg-group Group pools of overlapping segments
--homozyg-match {0.95} Identity threshold for allelic matching overlapping segments
--homozyg-verbose Display actual genotypes for each pool
     
Association analysis procedures
--assoc Case/control or QTL association
--fisher Fisher's exact (allelic) test
--model Cochran-Armitage and full-model C/C association
--model --fisher Exact full-model tests
     
--T2 Hotelling's T(2) multilocus test
     
--mh Cochran-Mantel-Haenszel SNPxDISEASE|STRATA
--mh2 Cochran-Mantel-Haenszel SNPxSTRATA|DISEASE
--bd Breslow-Day homogeneity of odds ratios test
--homog Partitioning chi-square homogeneity of odds ratios test
     
--gxe QTL interaction test (dichotomous covariate only)
     
--linear Test for quantitative traits and multiple covariates
--logistic Test for disease traits and multiple covariates
--genotypic Include dominance term in model, and 2df model
--dominant Fit dominant model for minor allele
--recessive Fit recessive model for minor allele
--condition {SNP} Include additive effect of SNP in model
--condition-list {filename} Include additive effects of these SNPs in model
--sex Include sex effect in model
--interaction Include SNP x covariate interactions
--test-all Joint test of all terms in model
--parameters {1,2,...} Fit only a subset of model terms
--tests {1,2,...} Joint test of user-specified set of parameters
--beta Make --logistic return coefficients, not odds ratios
     
--tdt Family-based TDT and parenTDT (permute TDT)
--parentdt1 As above, except permuted statistic is parental test
--parentdt2 As above, except permuted statistic is combined test
--poo Parent-of-origin analysis in TDT
     
--dfam Disease family-test (families and unrelateds)
     
--ci {0.95} Confidence interval for CMH odds ratios
     
--set-test Set-based association (requires --mperm)
--set-p {p-value} p-value threshold for set-based test
--set-r2 {r^2} R-squared threshold for set-based test
--set-max {N SNPs} Maximum number of SNPs in set
     
Permutation procedure options
--perm Run permutations (adaptive-mode)
--mperm {1000} # of permutations in max-perm mode
--aperm {...} Parameters (six) for adaptive permutation mode
--rank Modifies --mperm for rank-based permutation
     
--model-trend Use CA-trend test from --model
--model-gen Use genotypic test from --model
--model-dom Use dominant test from --model
--model-rec Use recessive test from --model
     
--genedrop Permutation by gene-dropping simulation (family-data)
--swap-parents Labal-swap permutation for parents when gene-dropping
--swap-sibs Labal-swap permutation for siblings when gene-dropping
--swap-unrel Labal-swap permutation for unrelateds when gene-dropping
     
--family Make Family ID the cluster
     
--p2 Alternate permutation scheme (C/C only)
     
Epistasis analysis
--epistasis Perform SNP x SNP epistatic analysis
--fast-epistasis Quick SNP x SNP screening for C/C data
--twolocus {SNP} {SNP} Display contingency table for two SNPs
--case-only Case-only epistatic analysis
--gap {1000} Gap (kb) for SNP x SNP case-only epistasis tests
--epi1 {0.0001} Output p-value threshold: pairs
--set-by-all Test set 1 SNPs paired with all others
--nop Do not calculate p-values (fast screening)
     
--genepi Gene-based test for epistasis
     
Haplotype inference and linkage disequilibrium
--hap-snps {snplist} Specify a list of SNPs to phase
--hap-window {N} Specify haplotype sliding window
--hap {tagfilename} Multimarker predictor / haplotype list
--whap {tagfilename} Weighted haplotype test list
     
--hap-assoc Perform haplotype-based case/control association
--hap-tdt Perform haplotype-based TDT
--hap-freq Output haplotype frequencies for entire sample
--hap-phase Output individual haplotype phases
--hap-phase-wide Output individual haplotype phases, wide-format
     
     
--hap-impute Create fileset with imputed haplotypes as SNPs
--hap-pp {0.8} Posterior probability threshold
--hap-miss {0.5} Proportion of missing genotypes allowed
--hap-min-phase-prob {0.01} Minimum reported phase probability
--hap-max-phase {N} Maximum number of phases considered per person
--mhf {0.01} Minor haplotype frequency threshold
     
Proxy association and imputation methods
--proxy-assoc {SNP/all} Proxy association methods
--proxy-glm Use linear models in proxy association
--proxy-drop Drop then re-impute observed genotypes
--proxy-tdt {SNP/all} Proxy TDT association methods
     
--proxy-impute {SNP/all} Proxy imputation methods
--proxy-replace Replace observed genotypes
--proxy-dosage Also output dosage file
--proxy-impute-threshold {0.95} Per-genotype threshold to impute for an individual
     
--proxy-list {file} Specify SNPs to impute/test
--proxy-flanking {file} Specify proxies for single reference SNP
     
--proxy-r2 {0 0.05 0.5} Proxy selection LD parameters
--proxy-maxsnp {5} Maximum number of proxies tto select
--proxy-window {15} Proxy SNP search space (SNPs)
--proxy-kb {250} Proxy SNP search space (kb)
     
--proxy-b-threshold {0.1} MAF threshold for rare alleles (plan B)
--proxy-b-r2 {0 0.05 0.5} Alternate proxy selection LD parameters
--proxy-b-maxsnp {0.1} Alternate maximum number of proxies to use
--proxy-b-window {0.1} Alternate proxy SNP search space (SNPs)
--proxy-b-kb {250} Alternate proxy SNP search space (kb)
     
--proxy-maf {0.01} Proxy SNP MAF threshold
--proxy-geno {0.05} Proxy SNP missingness threshold
--proxy-r2-no-filter No LD-based proxy selection
     
--proxy-mhf {0.05} Proxy haplotype frequency threshold
--proxy-sub-r2 {0.8} Minimum r-squared with reference for haplotypic proxies (verbose mode)
--proxy-sub-maxsnp {3} Maximum number of SNPs per haplotypic proxy (verbose mode)
     
--proxy-verbose Verbose mode
--proxy-show-proxies List actual proxies in non-verbose mode
--proxy-genotypic-concordance In imputation, show genotypic-specific concordance
     
Conditional haplotype association tests
--chap Main conditional-haplotype test command
--specific-haplotype {haplotype(s)} Test for specific haplogroup effect
--independent-effect {snp{s}} Test for independent effect
--control {snp(s)/haplotype(s)} Control for certain effects
     
--alt-snp Specify SNP groupings under alternate
--null-snp Specify SNP groupings under null
     
--alt-group Specify haplogroupings under alternate
--null-group Specify haplogroupings under null
     
--test-snp Drop 1 or more conditioning SNPs
--each-versus-others Each all haplogroup-specific p-values
--each-vs-others As above
     
LD-based result clumping
--clump {file(s)} Comma-delimited result files
--clump-p1 {1e-4} p-value threshold for index SNPs
--clump-p2 {1e-2} p-value threshold for clumped SNPs
--clump-r2 {0.2} r^2 (LD) threshold for clumping
--clump-kb {250} kb-threshold for clumping
     
--clump-replicate Only report multi-file clumps
--clump-best For each SNP in the first file, find the best proxy from the other files
--clump-verbose Specifty verbose output
--clump-range {filename} Add gene/region range information to clumped output
--clump-range-border {kb} Use a kb border around each gene/region
--clump-annotate {field(s)} Include these fields in verbose mode
--clump-field {field} Specifty p-value field other than P
--clump-index-first Only index based on first results file
--clump-allow-overlap Specify that a SNP can appear in more than one clump
     
Annotation and meta-analysis of results
--annotate {filename} Annotate result file
     
--meta-analysis {filenames} Meta-analysis of multiple result files
     
--gene-report {filename} Results file to perform gene-report on
--gene-list {filename} List of genes/regions for reporting
--gene-list-border {kb} Add a kb border aroud each gene/region
--gene-subset {filename} Only report on a subset of genes, listed here
--gene-report-empty Report genes without any informative SNPs
     
LD pruning and pairwise LD
--indep {N M VIF} VIF pruning (N-SNP window, shifted at M-SNP intervals)
--indep-pairwise {N M r^2} r^2 pruning (as above)
--r Pairwise SNPxSNP LD (r)
--r2 Pairwise SNPxSNP LD (r^2)
--ld-window {N} Limit pairwise SNPxSNP to within a N SNP window
     
Definition of SETs
--set {setfilename} SET definitions
--subset {filename} Only read of subset of SETs from --set
--set-table Output a SNP by SET matrix
     
Copy number variants (CNV) analysis
--gfile {fileset} Load generic variant file
--cfile {fileset} Load segmental CNV fileset (CNV, FAM, MAP)
--cnv-list {filename} Load segmental CNV list
     
--cnv-del Filter only deletions
--cnv-dup Filter only duplications
     
--cnv-intersect {filename} Include segments intersecting with regions
--cnv-exclude {filename} Exclude segments intersecting with regions
--cnv-disrupt Include/Exclude segments that start or stop within a gene/region
--cnv-count {filename} Count number of regions intersected by CNVs
--cnv-border {kb} Add a kb border around each region
     
--cnv-freq-excldue-above N Exclude CNVs overlapping regions with more than N CNVs
--cnv-freq-excldue-below N Exclude CNVs overlapping regions with fewer than N CNVs
--cnv-freq-excldue-exact N Exclude CNVs overlapping regions with exactly N CNVs
--cnv-freq-incldue-exact N Include CNVs overlapping regions with exactly N CNVs
--cnv-freq-method2 Use alternative method for determining CNV frequency
     
--cnv-overlap {N} Define overlap of CNV and region by CNV length
--cnv-union-overlap {N} Define overlap of CNV and region by union
--cnv-region-overlap {N} Define overlap of CNV and region by region length
     
--cnv-write Create a new CNV and FAM file
--cnv-write-freq Include frequency counts if --cnv-freq-method2 specified
--cnv-make-map Create a new MAP file from a CNV and FAM file
--cnv-report-regions List regions that are intersected by CNVs
--cnv-verbose-report-regions Verbose listing of regions that are intersected by CNVs
--cnv-subset {filename} Define overlap of CNV and region by region length
     
--cnv-track {kb} Create a UCSC-compatible BED track for viewing CNVs
--cnv-blue {kb} Make this CNV track blue
--cnv-red {kb} Make this CNV track red
--cnv-green {kb} Make this CNV track green
--cnv-brown {kb} Make this CNV track brown
     
--cnv-kb {N} Exclude segments below N kb
--cnv-max-kb {N} Exclude segments above N kb
--cnv-score {N} Exclude segments below N score
--cnv-max-score {N} Exclude segments above N score
     
--cnv-drop-no-segment Remove individuals with no segments
--cnv-unique Exclude CNVs seen in both cases and controls
--cnv-seglist {kb} Create a printout of CNVs
     
--cnv-indiv-perm Permutation test for genome-wide CNV burden
--cnv-test-2sided Use 2-sided approach for empirical p-values
--cnv-test-window {kb} Extend test to a region extending kb distance on either side of position
--cnv-test-region {kb} Test regions for CNV case/control differences
     
Data simulation options
--simulate {filename} Simulate SNP population-based data
--simulate-ncases {100} Number of cases to simulate
--simulate-ncontrols {100} Number of controls to simulate
--simulate-prevalence {0.01} Disease prevalence in population
--simulate-qt {filename} Simulate quantitative trait dataset
--simulate-label {label} Add identifier label to simulated individuals
--simulate-tags Simulate tags instead of causal variants
--simulate-haps Simulate causal variant / tag SNP pairs
     
--dummy {N} {M} Generate dataset of N individuals on M SNPs
     
Misc analysis output options
--adjust Output adjusted p-values and calculate genomic control
--lambda {X} Set lambda to X instead of estimating from data
--qq-plot Generate entries to faciliate a Q-Q plot in adjusted output
     
Misc.
--help Display list of options
--dog Set chromosome codes for dog
--mouse Set chromosome codes for mouse
--horse Set chromosome codes for horse
--cow Set chromosome codes for cow
--sheep Set chromosome codes for sheep
     
--lookup {SNP rs#} Lookup WGAS SNP annotation information
--lookup-gene {gene name} List all SNPs in gene
--lookup-list {snplist filename} SNP annotation for multiple SNPs

Output files (alphabetical listing: not up-to-date)

Filename Main associated command(s) Description
plink.adjust --adjust Adjusted significance values (multiple testing)
plink.assoc --assoc Association results
plink.assoc.hap --hap-assoc Haplotype-based association results
plink.assoc.linear --linear Linear regression model
plink.assoc.logistic --logistic Logistic regression model
plink.assoc.mperm --assoc --mperm maxT permutation empirical p-values
plink.assoc.perm --assoc --perm Adaptive permutation empirical p-values
plink.assoc.proxy --proxy-assoc Proxy association results
plink.assoc.set --assoc --set Set-based association results
plink.bed --make-bed Binary PED file
plink.bim --make-bed Binary MAP file
plink.chap --chap Conditional haplotype tests
plink.cov --write-covar Ordered, filtered covariate file
plink.clumped --clump LD-based results clumping
plink.clumped.best --clump-best Single best LD-based clumping
plink.clumped.ranges --clump-range Gene/region report for clumps
plink.cluster0 --cluster Progress of IBS clustering
plink.cluster1 --cluster IBS cluster solution, format 1
plink.cluster2 --cluster IBS cluster solution, format 2
plink.cluster3 --cluster IBS cluster solution, format 3
plink.cluster3.missing --cluster-missing IBM cluster solution, format 3
plink.cmh --mh Cochran-Mantel-Haenszel test 1
plink.cmh2 --mh2 Cochran-Mantel-Haenszel test 2
plink.cnv.indiv --cnv-list Copy number variant per individual summary
plink.cnv.overlap --cnv-list Copy number variant overlap
plink.cnv.summary --cnv-list Copy number variant summary
plink.cnv.summary.mperm --cnv-list Copy number variant test
plink.diff --merge-mode 6/7 Difference file
plink.epi-cc1 --epistasis Epistasis: case/control pairwise results
plink.epi-cc2 --epistasis Epistasis: case/control summary results
plink.epi-co1 --epistasis --case-only Epistasis: case-only pairwise results
plink.epi-co2 --epistasis --case-only Epistasis: case-only summary results
plink.fam --make-bed Binary FAM file
plink.fmendel --mendel Mendel errors, per family
plink.frq --freq Allele frequency table
plink.frq.count --freq --counts Allele counts table
plink.frq.hap --hap-freq Allele frequency table
plink.genepi.dat --genepi Gene-based epistasis R dataset
plink.genepi.R --genepi Gene-based epistasis R script
plink.genome --genome Genome-wide IBD/IBS pairwise measures
plink.het --het Individual inbreeding coefficients
plink.hh List of heterozygous haploid genotypes (SNPs/individuals)
plink.hom --homozyg-snp --homozyg-kb Runs of homozygosity
plink.hom.overlap --homozyg-group Pools of overlapping runs of homozygosity
plink.homog --homog Between strata homogeneity test
plink.hwe --hardy Hardy-Weinberg test statistics
plink.imendel --mendel Mendel errors, per individual
plink.imiss --missing Missing rates, per individual
plink.info --recodeHV Info file for Haploview filesets
plink.irem --mind List of individuals removed for low genotyping
plink.imputed.map --hap-impute Imputed from multi-marker predictors
plink.impute.ped --hap-impute Imputed from multi-marker predictors
plink.list --list Recoded LIST file
plink.lmendel --mendel Mendel errors, per locus
plink.lmiss --missing Missing rates, per locus
plink.log Log file (always generated)
plink.map --recode Recoded MAP file
plink.mdist --cluster --matrix IBS distance matrix
plink.mdist.missing --cluster-missing IBM distance matrix
plink.mendel --mendel Mendel errors, per error
plink.mishap --hap List of SNPs that show problem phasing (could not be found or on wrong chromosome)
plink.missing --test-missing Test of differences in C/C missing rates
plink.missing.hap --test-mishap Haplotype-based test of non-random genotyping failure
plink.missnp --merge List of SNPs that show strand problems when merging files (more than 2 alleles)
plink.model --model Full-model association results
plink.model.best.mperm --model --mperm Best full-model association max(T) permutation results
plink.model.best.perm --model --perm Best full-model association adaptive permutation results
plink.model.gen.mperm --model --mperm --model-gen Genotypic association max(T) permutation results
plink.model.gen.perm --model --perm --model-gen Genotypic association adaptive permutation results
plink.model.dom.mperm --model --mperm --model-dom Dominant association max(T) permutation results
plink.model.dom.perm --model --perm --model-dom Dominant association adaptive permutation results
plink.model.trend.mperm --model --mperm --model-trend Trend test association max(T) permutation results
plink.model.trend.perm --model --perm --model-trend Trend test association adaptive permutation results
plink.model.rec.mperm --model --mperm --model-rec Recessive association max(T) permutation results
plink.model.rec.perm --model --perm --model-rec Recessive association adaptive permutation results
plink.nof List of SNPs with no observed founders
plink.nosex List of individuals with ambiguous sex code
plink.nearest --cluster --neighbour Nearest neighbour (IBS) statistics
plink.pdump --pedigree Information on pedigree structure
plink.ped --recode Recoded PED file
plink.phase-* --hap --phase Haplotype phases (one file per locus)
plink.plist --plist Pairwise list of two people's genotypes
plink.proxy.impute --proxy-impute Proxy imputation output
plink.proxy.impute.dosage --proxy-impute --proxy-dosage Proxy imputation dosage output
plink.proxy.report --proxy-assoc Verbose proxy association output
plink.prune.in --indep --indep-pairwise List of remaining SNPs (i.e. not pruned)
plink.prune.out --indep --indep-pairwise List of pruned-out SNPs
plink.qassoc --assoc Quantitative trait association results
plink.qassoc.gxe --gxe Quantitative trait interaction results
plink.range.report --cnv-verbose-report-regions Listing of CNVs by genes/regions
plink.raw --recodeAD Recoded additive/dominance format file
plink.snplist --write-snplist List of SNPs in the dataset
plink.T2 --T2 Hotelling's T(2) test results
plink.tdt --tdt TDT/parenTDT asymptotic results
plink.tdt.hap --tdt TDT/parenTDT permutaion results
plink.tdt.mperm --tdt TDT/parenTDT max(T) permutation results
plink.tdt.perm --tdt TDT/parenTDT adaptive permutation results
plink.tdt.poo --tdt --poo TDT parent-of-origin results
plink.tdt.poo.mperm --tdt --poo --mperm TDT parent-of-origin max(T) permutation results
plink.tdt.poo.perm --tdt --poo --perm TDT parent-of-origin adaptive permutation results
plink.tdt.poo.set --tdt --poo --set --mperm TDT parent-of-origin set-based results
plink.tdt.set --tdt --set --mperm TDT/parenTDT set-based results
plink.tfam --transpose / --tfile FAM for for transposed fileset
plink.tped --transpose / --tfile PED file for transposed fileset
plink.twolocus --twolocus SNP x SNP contingency table
 
This document last modified Saturday, 10-Oct-2009 11:38:22 EDT