IBDseq specifications

Information


Unique identifier OMICS_05460
Name IBDseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for IBDseq

IBDseq in publications

 (5)
PMCID: 5586387
PMID: 28739658
DOI: 10.1534/genetics.117.1122

[…] of these methods may be due to their focus on identifying long stretches of identical haplotype segments that more readily discriminate recent shared relatedness from chance sharing of alleles. the ibdseq method, while performing well for inferring first- through seventh-degree relatives, infers a much larger fraction of pairs of individuals as related that are reported as unrelated, suggesting […]

PMCID: 5519631
PMID: 28729679
DOI: 10.1038/s41598-017-05445-3

[…] effects, inbreeding, and other population forces. such increases may increase imputation accuracy by improved phasing. to assess these phenomena in the agrp, we identified ibd and hbd regions with ibdseq, a method designed specifically to identify such regions in wgs data. to compare the ibd sharing among anabaptists, among other europeans, and between anabaptists and other europeans, […]

PMCID: 5490002
PMID: 28643794
DOI: 10.1038/ncomms15927

[…] and a longer generation time of 33 years. we then estimated more recent demographic changes (from the present to ∼9,000 years ago) using ibdne with the minimum-sample-size data set. we used ibdseq to detect ibd segments in sequence data from chromosome 2 in all populations. we then used ibdne with the default parameters and a minimum ibd segment length of 2 centimorgan (cm) units. […]

PMCID: 5062574
PMID: 27725671
DOI: 10.1038/ncomms12522

[…] singletons per individual in this sample (average=15,946 compared with the other sampling sites ranging 26,545–35,565). consistent with other patterns of bottlenecks in this population, we ran the ibdseq/ibdne pipeline using best practices recommended by the authors. we observe an elevation of median pairwise identity-by-descent (ibd) in the garifuna (167 mb), relative to an expected value […]

PMCID: 4856080
PMID: 26935417
DOI: 10.1534/g3.116.027581

[…] high-density array data, as the field develops algorithms aimed to detect even shorter segments due to the improved density of markers in the era of whole genome sequencing [e.g., programs like ibdseq ()], it seems imperative to note and reevaluate the potential problem of conflation. we found that ∼75–80% of the conflated segments are the result of pairs of segments existing in trans, […]


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IBDseq institution(s)
Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA

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