UNPHASED
Description
UNPHASED is a suite of programs for association analysis of multilocus haplotypes from unphased genotype data. UNPHASED features include:* Analysis of nuclear families and unrelated subjects, and combinations of the two
* Analysis of discrete or quantitative traits
* Maximum likelihood treatment of missing genotype data and uncertain haplotypes
* Global association tests and tests of individual haplotypes
* Conditioning tests that allow for previous associations of linked loci
* Inclusion of information from additional tag markers
* Support for non-genetic covariates including parent-of-origin
* Permutation tests allowing for multiple testingUNPHASED was developed by Frank Dudbridge at the MRC, Cambridge. Unphased website.
UNPHASED is intended to be used interactively on Helix. To run an UNPHASED job, log on to helix.nih.gov using ssh, and type unphased. The program will respond with a list of available parameters.
Version
The version number is displayed at the top of the Unphased output.
Sample session
(user input in bold):% unphased gh_ped.01 ***START OF UNPHASED 3.0.12*** Reading pedigree file gh_ped.01...done ANALYSIS OPTIONS Number of nuclear families: 13 Number of unrelated subjects: 0 Rare haplotype maximum frequency (-rare): 0 Zero haplotype maximum frequency (-zero): 1e-08 Quantitative trait variance (-variance): 1 Model normal distribution (-normal): N Restrict to certain haplotypes (-certain): N Estimate missing genotypes (-missing): N Test genotypes (-genotype): N Condition on genotype effects (-condgenotype): N Assume no prior linkage (-nolinkage): N Model odds ratio in parents (-parentrisk): N Use only one family based control (-onefbc): N Chromosome X (-chrX): N Chromosome Y (-chrY): N Convergence threshold (-epsilon): 1e-08 Numerical maximisation (-neldermead): D-F-P Random restarts (-restarts): 0 Random number seed (-randomseed): 1 Number of permutations (-permutation): 0 Permutation distribution quantile (-quantile): 5 OUTPUT OPTIONS Output file (-output): Brief output (-brief): N Output LD statistics (-LD): N Output permutation analyses (-permoutput): N Haplotype dump file (-dump): Just the most likely haplotypes (-mostlikely): N --------- ANALYSIS OF BINARY TRAIT: Disease Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (13 evaluations) Null likelihood...done (11 evaluations) Alternative likelihood...done (13 evaluations) MARKER OPTIONS Test marker: 1 TEST OF OVERALL ASSOCIATION Null log-likelihood = -6.748 Alternative log-likelihood = -6.578 Likelihood ratio chisq = 0.3398 df = 1 p-value = 0.5599 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 1 0.3333 0.1667 1 1 1 2 4 5 0.6667 0.8333 0.5 0.04534 5.514 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (2 evaluations) Null likelihood...done (2 evaluations) Alternative likelihood...done (2 evaluations) MARKER OPTIONS Test marker: 2 TEST OF OVERALL ASSOCIATION Null log-likelihood = -5.545 Alternative log-likelihood = -5.545 Likelihood ratio chisq = 0 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 2 0.5 0.5 1 1 1 2 2 2 0.5 0.5 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (61 evaluations) Null likelihood...done (17 evaluations) Alternative likelihood...done (61 evaluations) MARKER OPTIONS Test marker: 3 TEST OF OVERALL ASSOCIATION Null log-likelihood = -5.407 Alternative log-likelihood = -4.02 Likelihood ratio chisq = 2.773 df = 1 p-value = 0.09589 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 4 6 0.6667 1 1 1 1 2 2 0 0.3333 0 3.243e+08 3.243e+08 3.243e+08 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (10 evaluations) Null likelihood...done (2 evaluations) Alternative likelihood...done (10 evaluations) MARKER OPTIONS Test marker: 4 TEST OF OVERALL ASSOCIATION Null log-likelihood = -8.318 Alternative log-likelihood = -7.795 Likelihood ratio chisq = 1.046 df = 1 p-value = 0.3063 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 4 2 0.6667 0.3333 1 1 1 2 2 4 0.3333 0.6667 0.3333 0.03467 3.205 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (9 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (9 evaluations) MARKER OPTIONS Test marker: 5 TEST OF OVERALL ASSOCIATION Null log-likelihood = -6.945 Alternative log-likelihood = -6.945 Likelihood ratio chisq = -3.553e-15 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 2 0.3333 0.3333 1 1 1 2 4 4 0.6667 0.6667 1 0.1409 7.099 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (57 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (57 evaluations) MARKER OPTIONS Test marker: 6 TEST OF OVERALL ASSOCIATION Null log-likelihood = -7.638 Alternative log-likelihood = -6.252 Likelihood ratio chisq = 2.773 df = 1 p-value = 0.09589 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 3 1 0.5 0.1667 1 1 1 2 3 5 0.5 0.8333 0 0 0 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (1 evaluations) Null likelihood...done (1 evaluations) Alternative likelihood...done (1 evaluations) MARKER OPTIONS Test marker: 7 TEST OF OVERALL ASSOCIATION Null log-likelihood = 0 Alternative log-likelihood = 0 Likelihood ratio chisq = 0 df = 0 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 6 6 1 1 1 1 1 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (58 evaluations) Null likelihood...done (11 evaluations) Alternative likelihood...done (58 evaluations) MARKER OPTIONS Test marker: 8 TEST OF OVERALL ASSOCIATION Null log-likelihood = -6.748 Alternative log-likelihood = -4.669 Likelihood ratio chisq = 4.159 df = 1 p-value = 0.04142 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 3 0 0.5 0 1 1 1 2 3 6 0.5 1 0 0 0 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (9 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (9 evaluations) MARKER OPTIONS Test marker: 9 TEST OF OVERALL ASSOCIATION Null log-likelihood = -7.638 Alternative log-likelihood = -7.638 Likelihood ratio chisq = -1.776e-15 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 4 4 0.6667 0.6667 1 1 1 2 2 2 0.3333 0.3333 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (55 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (55 evaluations) MARKER OPTIONS Test marker: 10 TEST OF OVERALL ASSOCIATION Null log-likelihood = -8.15 Alternative log-likelihood = -7.457 Likelihood ratio chisq = 1.386 df = 1 p-value = 0.239 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 3 0.3333 0.5 1 1 1 2 4 3 0.6667 0.5 1.561e+08 1.561e+08 1.561e+08 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (9 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (9 evaluations) MARKER OPTIONS Test marker: 11 TEST OF OVERALL ASSOCIATION Null log-likelihood = -7.638 Alternative log-likelihood = -7.638 Likelihood ratio chisq = 0 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 2 0.3333 0.3333 1 1 1 2 4 4 0.6667 0.6667 1 1 1 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (11 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (11 evaluations) MARKER OPTIONS Test marker: 12 TEST OF OVERALL ASSOCIATION Null log-likelihood = -8.15 Alternative log-likelihood = -7.98 Likelihood ratio chisq = 0.3398 df = 1 p-value = 0.5599 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 3 0.3333 0.5 1 1 1 2 4 3 0.6667 0.5 2 0.1813 22.06 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (64 evaluations) Null likelihood...done (20 evaluations) Alternative likelihood...done (64 evaluations) MARKER OPTIONS Test marker: 13 TEST OF OVERALL ASSOCIATION Null log-likelihood = -3.442 Alternative log-likelihood = -2.749 Likelihood ratio chisq = 1.386 df = 1 p-value = 0.239 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 0 1 0 0.1667 1 1 1 2 6 5 1 0.8333 1.716e+08 1.716e+08 1.716e+08 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (12 evaluations) Null likelihood...done (12 evaluations) Alternative likelihood...done (12 evaluations) MARKER OPTIONS Test marker: 14 TEST OF OVERALL ASSOCIATION Null log-likelihood = -3.806 Alternative log-likelihood = -3.806 Likelihood ratio chisq = 0 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 3 3 0.75 0.75 1 1 1 2 1 1 0.25 0.25 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (17 evaluations) Null likelihood...done (17 evaluations) Alternative likelihood...done (17 evaluations) MARKER OPTIONS Test marker: 15 TEST OF OVERALL ASSOCIATION Null log-likelihood = -5.407 Alternative log-likelihood = -5.407 Likelihood ratio chisq = -1.776e-15 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 1 1 0.1667 0.1667 1 1 1 2 5 5 0.8333 0.8333 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (12 evaluations) Null likelihood...done (12 evaluations) Alternative likelihood...done (12 evaluations) MARKER OPTIONS Test marker: 16 TEST OF OVERALL ASSOCIATION Null log-likelihood = -4.499 Alternative log-likelihood = -4.499 Likelihood ratio chisq = 0 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 3 3 0.75 0.75 1 1 1 2 1 1 0.25 0.25 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (9 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (9 evaluations) MARKER OPTIONS Test marker: 17 TEST OF OVERALL ASSOCIATION Null log-likelihood = -6.945 Alternative log-likelihood = -6.945 Likelihood ratio chisq = -5.329e-15 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 4 4 0.6667 0.6667 1 1 1 2 2 2 0.3333 0.3333 1 0.1409 7.099 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (17 evaluations) Null likelihood...done (17 evaluations) Alternative likelihood...done (17 evaluations) MARKER OPTIONS Test marker: 18 TEST OF OVERALL ASSOCIATION Null log-likelihood = -5.407 Alternative log-likelihood = -5.407 Likelihood ratio chisq = -3.553e-15 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 1 1 0.1667 0.1667 1 1 1 2 5 5 0.8333 0.8333 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (9 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (9 evaluations) MARKER OPTIONS Test marker: 19 TEST OF OVERALL ASSOCIATION Null log-likelihood = -7.638 Alternative log-likelihood = -7.638 Likelihood ratio chisq = -1.776e-15 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 2 0.3333 0.3333 1 1 1 2 4 4 0.6667 0.6667 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (11 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (11 evaluations) MARKER OPTIONS Test marker: 20 TEST OF OVERALL ASSOCIATION Null log-likelihood = -8.15 Alternative log-likelihood = -7.98 Likelihood ratio chisq = 0.3398 df = 1 p-value = 0.5599 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 3 2 0.5 0.3333 1 1 1 2 3 4 0.5 0.6667 0.5 0.04534 5.514 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (55 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (55 evaluations) MARKER OPTIONS Test marker: 21 TEST OF OVERALL ASSOCIATION Null log-likelihood = -8.15 Alternative log-likelihood = -7.457 Likelihood ratio chisq = 1.386 df = 1 p-value = 0.239 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 4 3 0.6667 0.5 1 1 1 2 2 3 0.3333 0.5 0 0 0 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (12 evaluations) Null likelihood...done (12 evaluations) Alternative likelihood...done (12 evaluations) MARKER OPTIONS Test marker: 22 TEST OF OVERALL ASSOCIATION Null log-likelihood = -4.499 Alternative log-likelihood = -4.499 Likelihood ratio chisq = 0 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 3 3 0.75 0.75 1 1 1 2 1 1 0.25 0.25 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (2 evaluations) Null likelihood...done (2 evaluations) Alternative likelihood...done (2 evaluations) MARKER OPTIONS Test marker: 23 TEST OF OVERALL ASSOCIATION Null log-likelihood = -5.545 Alternative log-likelihood = -5.545 Likelihood ratio chisq = 0 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 2 0.5 0.5 1 1 1 2 2 2 0.5 0.5 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (54 evaluations) Null likelihood...done (2 evaluations) Alternative likelihood...done (54 evaluations) MARKER OPTIONS Test marker: 24 TEST OF OVERALL ASSOCIATION Null log-likelihood = -5.545 Alternative log-likelihood = -4.159 Likelihood ratio chisq = 2.773 df = 1 p-value = 0.09589 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 1 3 0.25 0.75 1 1 1 2 3 1 0.75 0.25 3.33e+08 3.33e+08 3.33e+08 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (9 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (9 evaluations) MARKER OPTIONS Test marker: 25 TEST OF OVERALL ASSOCIATION Null log-likelihood = -7.638 Alternative log-likelihood = -7.638 Likelihood ratio chisq = 0 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 4 4 0.6667 0.6667 1 1 1 2 2 2 0.3333 0.3333 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (58 evaluations) Null likelihood...done (16 evaluations) Alternative likelihood...done (58 evaluations) MARKER OPTIONS Test marker: 26 TEST OF OVERALL ASSOCIATION Null log-likelihood = -3.014 Alternative log-likelihood = -2.321 Likelihood ratio chisq = 1.386 df = 1 p-value = 0.239 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 1 0 0.25 0 1 1 1 2 3 4 0.75 1 0 0 0 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (55 evaluations) Null likelihood...done (11 evaluations) Alternative likelihood...done (55 evaluations) MARKER OPTIONS Test marker: 27 TEST OF OVERALL ASSOCIATION Null log-likelihood = -6.748 Alternative log-likelihood = -6.055 Likelihood ratio chisq = 1.386 df = 1 p-value = 0.239 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 2 1 0.3333 0.1667 1 1 1 2 4 5 0.6667 0.8333 0 0 0 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (17 evaluations) Null likelihood...done (17 evaluations) Alternative likelihood...done (17 evaluations) MARKER OPTIONS Test marker: 28 TEST OF OVERALL ASSOCIATION Null log-likelihood = -5.407 Alternative log-likelihood = -5.407 Likelihood ratio chisq = -3.553e-15 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 1 1 0.1667 0.1667 1 1 1 2 5 5 0.8333 0.8333 1 0.06255 15.99 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (1 evaluations) Null likelihood...done (1 evaluations) Alternative likelihood...done (1 evaluations) MARKER OPTIONS Test marker: 29 TEST OF OVERALL ASSOCIATION Null log-likelihood = 0 Alternative log-likelihood = 0 Likelihood ratio chisq = 0 df = 0 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 4 4 1 1 1 1 1 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (64 evaluations) Null likelihood...done (20 evaluations) Alternative likelihood...done (64 evaluations) MARKER OPTIONS Test marker: 30 TEST OF OVERALL ASSOCIATION Null log-likelihood = -3.442 Alternative log-likelihood = -2.749 Likelihood ratio chisq = 1.386 df = 1 p-value = 0.239 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 0 1 0 0.1667 1 1 1 2 6 5 1 0.8333 1.716e+08 1.716e+08 1.716e+08 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (57 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (57 evaluations) MARKER OPTIONS Test marker: 31 TEST OF OVERALL ASSOCIATION Null log-likelihood = -7.638 Alternative log-likelihood = -6.252 Likelihood ratio chisq = 2.773 df = 1 p-value = 0.09589 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 5 3 0.8333 0.5 1 1 1 2 1 3 0.1667 0.5 0 0 0 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (9 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (9 evaluations) MARKER OPTIONS Test marker: 32 TEST OF OVERALL ASSOCIATION Null log-likelihood = -7.638 Alternative log-likelihood = -7.638 Likelihood ratio chisq = 0 df = 1 p-value = 1 ESTIMATES OF ALLELE EFFECTS Reference allele: 1 Allele Case Control Ca-Freq Co-Freq Odds-R 95%Lo 95%Hi 1 4 4 0.6667 0.6667 1 1 1 2 2 2 0.3333 0.3333 1 0.1409 7.099 --------- Exploratory pass...done Identifying rare haplotypes: Alternative likelihood...done (57 evaluations) Null likelihood...done (9 evaluations) Alternative likelihood...done (57 evaluations)
Documentation
- The options available for Unphased can be listed simply by typing unphased with no parameters.
- UNPHASED documentation at the MRC website.
