"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