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ANCESTRYMAP specifications


Unique identifier OMICS_02083
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for ANCESTRYMAP



Genome Wide Association of Copy Number Polymorphisms and Kidney Function

PLoS One
PMCID: 5279752
PMID: 28135296
DOI: 10.1371/journal.pone.0170815

[…] ucture as covariates (Methods). Because global differences in allele frequencies may exist between subpopulations particularly within the AA cohort, we estimated the percentage of African ancestry by ANCESTRYMAP[] using genotypes from 1401 ancestry-informative markers in 2,152 AA participants. For the AA cohort, none of the AA CNPs are statistically significant with or without global ancestry adju […]


Genome Wide Interaction with Insulin Secretion Loci Reveals Novel Loci for Type 2 Diabetes in African Americans

PLoS One
PMCID: 4957757
PMID: 27448167
DOI: 10.1371/journal.pone.0159977

[…] 2D studies, PCs were computed for each study using high-quality SNPs as previously described [,–,]. The first PC was highly correlated (r2 >0.87) with global African-European ancestry, as measured by ANCESTRYMAP [], STRUCTURE [], or FRAPPE []. The African American T2D study samples had an average of 80% African ancestry. By analyzing unrelated samples from all studies using SMARTPCA [], only the f […]


Strong Selection at MHC in Mexicans since Admixture

PLoS Genet
PMCID: 4749250
PMID: 26863142
DOI: 10.1371/journal.pgen.1005847

[…] HGDP) [], is an inaccurate ancestral population for Puerto Ricans, which might produce artifacts in local ancestry inference. Third, Price and colleagues analyzed a larger sample using their software AncestryMap [] and did not discover the deviation of local ancestry reported by Tang and colleagues.We would like to make the following comments. First, the AncestryMap uses the so called ancestry inf […]


Mapping asthma associated variants in admixed populations

Front Genet
PMCID: 4586512
PMID: 26483834
DOI: 10.3389/fgene.2015.00292

[…] Well-established first generation admixture analysis tools for from sparse AIMs panels (e.g., ANCESTRYMAP, ADMIXMAP) are used in asthma to identify genomic regions that differ significantly between ancestries (Hoggart et al., ; Patterson et al., ). Like local and global ancestry tools, Hidden […]


Admixture mapping of tuberculosis and pigmentation related traits in an African–European hybrid cattle population

Front Genet
PMCID: 4467177
PMID: 26124773
DOI: 10.3389/fgene.2015.00210

[…] ed in a position intermediate to the parental and outlying populations. For each individual a local and a genome-wide ancestry, indicated by the proportion of European Bos taurus, was estimated using ANCESTRYMAP () using a burn-in period of 100 iterations with 200 follow-on iterations. The stability of the result was monitored by increasing the burn-in period and follow-on iterations by a factor o […]


ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium

BMC Genet
PMCID: 4408589
PMID: 25886794
DOI: 10.1186/s12863-015-0179-y

[…] quencing has decreased, MALD studies have become more common and successfully applied to identify a number of genetic variants associated with common diseases []. Several software packages, ADMIXMAP, ANCESTRYMAP and STRUCTURE, provided good estimates of global ancestry (i.e. the proportion of ancestors from each admixing population for an individual), as well as statistics for association between […]


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ANCESTRYMAP institution(s)
Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA


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