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SABER specifications

Information


Unique identifier OMICS_02081
Name SABER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Hua Tang

Publication for SABER

SABER citations

 (15)
library_books

Toward high resolution population genomics using archaeological samples

2016
PMCID: 4991838
PMID: 27436340
DOI: 10.1093/dnares/dsw029

[…] ntial to partition the genome into haplotypes with distinct ancestries that may have been inherited from multiple populations. Such haplotypes can be obtained using ‘local ancestry’ tools (HAPMIX, or SABER, LAMP, and MULTIMIX and others) which allow inference of ‘local ancestry’ instead of the ‘global ancestry’ (that can be inferred with PCA, SPAMIX, GPS, ADMIXTURE, STRUCTURE, reAdmix) and their u […]

library_books

Strong Selection at MHC in Mexicans since Admixture

2016
PLoS Genet
PMCID: 4749250
PMID: 26863142
DOI: 10.1371/journal.pgen.1005847

[…] nd colleagues analyzed a small cohort of Puerto Rican samples and reported three regions that are under strong recent selection []. Using their then state-of-the-art local ancestry inference software Saber [], Tang and colleagues discovered in Puerto Rican samples genomic regions whose mean local ancestries (averaged over individuals) significantly deviated from the genome-wide average—a hallmark […]

library_books

Admixture mapping of coronary artery calcification in African Americans from the NHLBI family heart study

2015
BMC Genet
PMCID: 4417236
PMID: 25902833
DOI: 10.1186/s12863-015-0196-x

[…] rely on reference allele frequencies for each parental population (i.e. LAMP [] and those methods that utilize reference haplotypes for each of the ancestral populations (i.e. HAPMIX [], LAMP-LD [], Saber []) []. Shriner et al. [] suggest that LAMP-LD is among the most accurate software for local ancestry inference.In the current study, local ancestry was inferred using LAMP-LD []. Each chromosom […]

library_books

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

2015
BMC Genet
PMCID: 4408589
PMID: 25886794
DOI: 10.1186/s12863-015-0179-y

[…] lack of local LD among sampled markers. This reliance on sparse marker sets results from the additional complexity involved with the modeling of local LD. An attempt was made in one software package, SABER, to model 2-way LD of a marker with its immediate neighbors, but this was later shown to allow bias into the model from higher order local LD with more distantly linked markers [,]. The conseque […]

library_books

The Role of Local Ancestry Adjustment in Association Studies Using Admixed Populations

2014
Genet Epidemiol
PMCID: 5079159
PMID: 25043967
DOI: 10.1002/gepi.21835

[…] MAP [], ADMIXMAP [], ADMIXPROGRAM [], and MALDsoft []) use ancestry informative markers to track the ancestry variation across genome. LAMP [] and WINPOP [] incorporated unlinked GWAS chip genotypes. SABER [] accounted for ancestral LD and allowed denser SNPs. HAPMIX [] and HAPAA [] employed phased haplotypes, which largely improved the accuracy at the price of considerable computational complexit […]

library_books

Inferring ancestry from population genomic data and its applications

2014
Front Genet
PMCID: 4080679
PMID: 25071832
DOI: 10.3389/fgene.2014.00204

[…] leverage the information that is available in haplotypes which can potentially be useful for distinguishing closely related populations. In contrast other methods that can explicitly model LD [e.g., SABER: ; HAPAA (HMM-based analysis of polymorphisms in admixed ancestries): ; HAPMIX: ] are computationally intensive and are able to consider only two ancestral populations at a time. LAMP (local anc […]

Citations

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SABER institution(s)
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

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