[an error occurred while processing this directive] Options

Option	Parameter	Description
--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
--test-missing
--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
--parentdt1
--parentdt2
--epistasis
--case-only
--epi1	{0.0001}
--epi2	{0.01}
--set-by-all
--genepi
--R
--nop
--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

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Output files

Filename	Description
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
plink-recode.map	Recoded MAP file
plink-extract.ped	Extracted PED file
plink-extract.map	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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