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hapassoc specifications


Unique identifier OMICS_10167
Name hapassoc
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2-8
Stability Stable
Maintained Yes


No version available


  • person_outline Kelly Burkett

Publications for hapassoc

hapassoc citations


Genome Wide Association Study of Serum 25 Hydroxyvitamin D in US Women

Front Genet
PMCID: 5838824
PMID: 29545823
DOI: 10.3389/fgene.2018.00067
call_split See protocol

[…] ispanic whites and African-Americans due to concerns about population stratification and racial differences in linkage disequilibrium (Stram and Seshan, ). We used expectation-maximization software (“hapassoc” package in R; Burkett et al., , ) to estimate haplotype frequencies and the association between 25(OH)D and each copy of the index haplotype, relative to the most common haplotype in non-His […]


Logistic Bayesian LASSO for Genetic Association Analysis of Data from Complex Sampling Designs

J Hum Genet
PMCID: 5572548
PMID: 28424482
DOI: 10.1038/jhg.2017.43

[…] gher proportion of current smokers amongst cases than in controls for both whites and blacks. More details about these data can be found in Hofmann et al. Haplotype frequencies as estimated using the hapassoc software based on maximum likelihood estimation are shown in . They vary substantially between the two races as well as between cases and controls. These estimates are used as starting values […]


Association of rare haplotypes on ULK4 and MAP4 genes with hypertension

BMC Proc
PMCID: 5133474
PMID: 27980663
DOI: 10.1186/s12919-016-0057-2
call_split See protocol

[…] The three standard approaches considered here—haplo.score, haplo.glm, and hapassoc—are based on the generalized linear model (GLM). In haplo.score, a global test of association as well as individual haplotype-specific tests are carried out using a score function. It estimat […]


Von Willebrand Factor Gene Variants Associate with Herpes simplex Encephalitis

PLoS One
PMCID: 4880288
PMID: 27224245
DOI: 10.1371/journal.pone.0155832
call_split See protocol

[…] Association of genotypes in the Scandinavian 115 HSE cases, EIMS 217 MS cases and 211 controls who were positive for HSV-1 IgG was tested using the assoc and hapassoc commands in PLINK v1.06 (http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml). P-values have not been corrected for multiple comparisons. The same analysis was performed including all indi […]


Above and beyond state of the art approaches to investigate sequence data: summary of methods and results from the population based association group at the Genetic Analysis Workshop 19

BMC Genet
PMCID: 4895250
PMID: 26866664
DOI: 10.1186/s12863-015-0310-0
call_split See protocol

[…] sociations with rare haplotypes in 2 hypertension-associated genes, ULK4 and MAP4. They analyzed sliding haplotype windows of 5 variants using 4 haplotype association methods: haplo.score, haplo.glm, hapassoc, and logistic Bayesian LASSO (LBL) and the three collapsing methods (SKAT, SKAT-O and SKAT-RC, see Tables  and ). LBL models the probability of haplotypes given disease status. Unobserved hap […]


Analysis of Social and Genetic Factors Influencing Heterosexual Transmission of HIV within Serodiscordant Couples in the Henan Cohort

PLoS One
PMCID: 4465854
PMID: 26068906
DOI: 10.1371/journal.pone.0129979
call_split See protocol

[…] chran Armitage tests with the coin package []. For haplotype analysis, maximum likelihood estimates of trait associations with SNP haplotypes were measured using the method of Burkett et al. with the hapassoc package []. Linkage analysis of the CCR2-CCR5 alleles was performed with Haploview []. […]


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