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Protocols

fastPHASE specifications

Information


Unique identifier OMICS_08921
Name fastPHASE
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for fastPHASE

fastPHASE citations

 (319)
library_books

Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

2018
BMC Genomics
PMCID: 5918591
PMID: 29695245
DOI: 10.1186/s12864-018-4690-1

[…] ters of an individual are automatically learnt from the data. However, this approach requires specifying the number K of haplotype clusters. Applying the cross-validation procedure implemented in the fastPHASE software to genotype data from G0, we set this number to 12 (option -K). We inferred haplotype clusters using 50 Expectation-Maximisation (EM) runs (option –nfit). Following Fariello et al. […]

library_books

Canine NAPEPLD associated models of human myelin disorders

2018
Sci Rep
PMCID: 5895582
PMID: 29643404
DOI: 10.1038/s41598-018-23938-7

[…] ly a fast score test (GenABEL) for association corrected for possible stratification by principal components was performed. Haplotypes around the significantly associated locus were constructed using fastPHASE. All genome positions refer to the CanFam3.1 reference sequence assembly. […]

call_split

Homo sapiens Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population

2018
Genome Biol Evol
PMCID: 5952923
PMID: 29608725
DOI: 10.1093/gbe/evy052
call_split See protocol

[…] mes Project Phase3 data was employed to see the trend of natural selection among the human population (). Unphased VCF files from 1000 Genomes Project were converted to phased haplotype files through fastPHASE (). In order to generate analysis that highlights the segregating alleles to be under the influence of positive selection, extended haplotype homozygosity (EHH) plots and relative EHH (rEHH) […]

library_books

Whole genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi feralization

2018
GigaScience
PMCID: 5905515
PMID: 29668959
DOI: 10.1093/gigascience/giy019

[…] Furthermore, the cross-population extended haplotype homozygosity [] was estimated between PT vs MGS, OL vs MGS, VT vs MGS, and BY vs MGS for candidate sweep region, based on haplotype data phased by fastPHASE []. GO functional enrichment analysis of the candidate genes was performed using ClueGO [], in which the P values were corrected using the Benjamini-Hochberg approach (). Then, a list of can […]

library_books

Convergent genomic signatures of domestication in sheep and goats

2018
Nat Commun
PMCID: 5840369
PMID: 29511174
DOI: 10.1038/s41467-018-03206-y

[…] rmation, hapFLK uses the Scheet and Stephens’ multipoint model for multilocus genotypes that can be fitted to unphased data. One of the main applications of this model is to perform phase estimation (fastPHASE software). In our analysis, the model was trained on unphased data, and therefore our analysis accounts for phase uncertainty. The method was used to regroup local haplotypes along chromosom […]

library_books

Mapping of a Major QTL for Ceratocystis Wilt Disease in an F1 Population of Theobroma cacao

2018
Front Plant Sci
PMCID: 5817064
PMID: 29491879
DOI: 10.3389/fpls.2018.00155

[…] × “K 101”) and the fifth cross includes two diversity panel members, “IMC 67” × “ICS 95.” In addition, a set of 31 diversity panel members from distinct Theobroma cacao structural groups was run with fastPhase (Scheet and Stephens, ). Two sets of markers were phased; the first set, contained the three markers in the Ceratocystis wilt QTL region on chromosome VI. The second set of markers included […]

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fastPHASE institution(s)
Department of Statistics, University of Washington, Seattle

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