PLINK: Whole genome data analysis toolset [an error occurred while processing this directive] Options

--file {fileroot} Specify .ped and .map files
--ped {pedfile} Specify .ped file
--map {mapfile} Specify .map file
--bfile {fileroot} Specify .bed, .fam and .map
--pheno {phenofile} Specify .phe file
--cov {covarfile} Specify .cov file
--output {fileroot} Specify output root filename
--out {fileroot} Specify output root filename
--make-bed Make .bed, .fam and .bim
--extract {snplist} Extract list of SNPs
--remove {indlist} Remove these individuals
--recode Output new PED and MAP files
--recode12 As above, with 1/2 alleles
--merge {pedfile} {mapfile} Merge two PED/MAP files
--restrand Flip all SNPs
--flip {snplist} Flip strand of SNPs in list
--maf {0.02} Minor allele frequency
--geno {0.1} Maximum per-SNP missing
--mind {0.1} Maximum per-person missing
--cell {5} Minimum genotype cell count for --model
--freq Save allele frequencies
--missing Missing rates (per individual/SNP)
--hardy Hardy-Weinberg disequilibrium tests
--perm {1000} # of permutations
--within Within cluster permutation
--family Make Family ID the cluster
--within-file {file} File containing clusters
--missing-genotype {0} Missing genotype code
--missing-phenotype {-9} Missing phenotype code
--ignore Do not perform analysis
--genome Output genome-wide IBS
--inbreeding Individual inbreeding
--homo-run N
--homo-run-snps N
--local-homo N sliding window of homozygosity
--cluster Perform clustering
--matrix Output distance matrices
--mc {0} Maximum cluster size
--cc Cluster by phenotype
--sol {N} Only analyse these subjects
--pmerge {0.01} Cluster merge value
--ibs Cluster on IBS, not p-value
--assoc Case/control, QT association
--model Full-model C/C association
--tdt Family-based TDT association
--epi1 {0.0001}
--epi2 {0.01}
--tag {tagfilename} Multimarker predictor list
--hap {tagfilename} Multimarker predictor list
--r Matrix of LD stats (r)
--r2 Matrix of LD stats (r^2)
--set {setfilename} SET definitions
--sharing IBS-based association
--boot Bootstrap z-scores
--help Display this list

Output files

plink.assoc Association results, with permutation
plink.cluster0 Progress of IBS clustering
plink.cluster1 IBS cluster solution, format 1
plink.cluster2 IBS cluster solution, format 2
plink.cluster3 IBS cluster solution, format 3
plink.mdist IBS distance matrix
plink.pdist p-value distance matrix
plink.imiss Missing rates, per individual
plink.lmiss Missing rates, per locus
plink.imendel Mendel errors, per family
plink.lmendel Mendel errors, per locus
plink.het Individual inbreeding coefficients
plink.ihet Runs of homozygosity
plink.frq Allele frequency table
plink.hwe Hardy-Weinberg test statistics
plink.tdt.asym TDT/parenTDT asymptotic results
plink.tdt.perm TDT/parenTDT permutaion results
plink.qassoc Quantitative trait association results
plink.model Full-model association results
plink.genome Genome-wide IBD/IBS pairwise measures
plink-recode.ped Recoded PED file Recoded MAP file
plink-extract.ped Extracted PED file Extracted MAP file
plink.epi-cc1 Epistasis: case/control pairwise results
plink.epi-cc2 Epistasis: case/control summary results
plink.epi-co1 Epistasis: case-only pairwise results
plink.epi-co2 Epistasis: case-only summary results
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