"Data management"> "Create new PED/MAP fileset (reordered)"> "Preserve original allele coding"> pom2.php?m=recode "Recode genotypes 11, 12 and 22 (00 missing)"> pom2.php?m=recode12 "Create a binary bED fileset"> pom2.php?m=makebed "Merge two PED files"> "Output standard PED/MAP fileset"> pom2.php?m=merge&p=1 "Output a binary bED fileset"> pom2.php?m=merge&p=2 "Extract a subset of SNPs"> "Output standard PED/MAP fileset"> pom2.php?m=extract&p=1 "Output a binary bED fileset"> pom2.php?m=extract&p=2 "Exclude a subset of SNPs"> "Output standard PED/MAP fileset"> pom2.php?m=exclude&p=1 "Output a binary bED fileset"> pom2.php?m=exclude&p=2 "Extract a subset of individuals"> "Output standard PED/MAP fileset"> pom2.php?m=keep&p=1 "Output a binary bED fileset"> pom2.php?m=keep&p=2 "Exclude of subset of individuals"> "Output standard PED/MAP fileset"> pom2.php?m=remove&p=1 "Output a binary bED fileset"> pom2.php?m=remove&p=2 "Flip SNP strand"> "Output standard PED/MAP fileset"> pom2.php?m=flip&p=1 "Output a binary bED fileset"> pom2.php?m=flip&p=2 "Missingness rates"> "SNP and individual missing rates"> pom2.php?m=missing "Test for different rates between cases and controls"> pom2.php?m=test-missing "Allele frequencies"> pom2.php?m=freq "Hardy-Weinberg equilibrium tests"> "Ignore phenotype"> pom2.php?m=hardy&p=1 "Stratify by case/control statues"> pom2.php?m=hardy&p=2 "Mendel error rates for nuclear family data"> pom2.php?m=mendel "IBS distance-based clustering"> "Cluster on genome-wide IBS"> pom2.php?m=cluster&p=1 "Cluster on genome-wide IBS and external matching criteria"> pom2.php?m=cluster&p=2 "IBD estimation (genome-wide)"> pom2.php?m=genome "Heterozygosity / inbreeding coefficients"> pom2.php?m=inbreeding "Runs of homozygosity"> pom2.php?m=homo-run-snps Pairwise r and r-squared pom2.php?m=ld-r "Haplotype inference"> "Calculate haplotype frequencies"> pom2.php?m=hap&p=1 "List individuals' haplotype phases"> pom2.php?m=hap&p=2 "Test case/control haplotype association"> pom2.php?m=hap&p=3 "Create imputed most-likely haplotype dataset"> pom2.php?m=hap&p=4 "Single SNP analyses"> "Population based sample"> "Disease trait"> "Basic allelic test"> "Without permutation"> pom2.php?m=assoc&p=1 "With adaptive permutation"> pom2.php?m=assoc&p=2 "With maxT permutation"> pom2.php?m=assoc&p=3 "Cochran-Armitage trend test and genotypic test"> "Without permutation"> pom2.php?m=model&p=1 "With adaptive permutation"> pom2.php?m=model&p=2 "With maxT permutation"> pom2.php?m=model&p=3 "Stratified/clustered sample tests"> "Within-cluster permutation"> pom2.php?m=within-file "Cochran-Mantel-Haenszel tests"> "SNP-disease assocation conditional on cluster"> pom2.php?m=mh1 "SNP-cluster association conditional on disease"> pom2.php?m=mh2 "Homogeneity of odds ratio tests"> pom2.php?m=homog "Quantitative trait"> "Without permutation"> pom2.php?m=qt&p=1 "With adaptive permutation"> pom2.php?m=qt&p=2 "With maxT permutation"> pom2.php?m=qt&p=3 "Within-cluster permutation"> "With adaptive permutation"> pom2.php?m=qt-within-file&p=2 "With maxT permutation"> pom2.php?m=qt-within-file&p=3 "Family-based sample"> "Disease traits: TDT analysis"> "Single SNP TDT only"> pom2.php?m=tdt&set=no "Single SNP and set-based TDT"> pom2.php?m=tdt&set=true "Quantitative trait: gene-dropping permutation"> "Gene-drop from founders"> pom2.php?m=qtdt&p=1 "Gene-drop from parents"> pom2.php?m=qtdt&p=2 "Epistatic analyses"> "SNP x SNP epistasis"> "Case-only analysis"> pom2.php?m=epi&p=1 "Case/control analysis"> pom2.php?m=epi&p=2 "Gene-based epistasis"> "Case-only analysis"> pom2.php?m=genepi&p=1 "Case/control analysis"> pom2.php?m=genepi&p=2