fastPHASE protocols

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fastPHASE statistics

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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 in pipelines

 (16)
2017
PMCID: 5433978
PMID: 28515876
DOI: 10.1002/ece3.2935

[…] eq consensus sequences for the xdh‐like region (nt_176739.1:340,370‐357,224) in igv (robinson et al., ), manually removed introns and other sites with missing data, and phased the sequences using the fastphase algorithm (scheet & stephens, ) in dnasp v5.10.1 (librado & rozas, ), resulting in 41 complete sequences (40 b. bifarius haplotypes and the b. impatiens reference) of length 4,049 bp […]

2017
PMCID: 5488459
PMID: 28486572
DOI: 10.1590/1678-4685-GMB-2016-0180

[…] (), we removed snvs that were no longer variable or that were represented just once in the dataset (i.e., singletons). the missing alleles were imputed and mc1r haplotypes were inferred by using fastphase (). a subset of the differences in genotype calling between the two approaches (unifiedgenotyper and haplotypecaller) were visually inspected by checking the bam files alignment by using […]

2017
PMCID: 5636130
PMID: 29020049
DOI: 10.1371/journal.pone.0186273

[…] statistical methods to infer haplotype phase, and prepares adequately the phased data for subsequent analyses. dnasp reconstructs the haplotype phase by applying various algorithms (phase v2.1, fastphase v1.1 and hapar) differing in the underlying population genetic assumptions []. nucleotide diversity estimates the average pairwise differences among sequences, based on all sites. tajima’s […]

2017
PMCID: 5919744
PMID: 29255118
DOI: 10.1534/g3.117.300199

[…] bayesb, prediction ability ranged from 0.09 to 0.66 (). imputation resulted in slightly higher prediction abilities for all traits, except for number of days to budding. the prediction ability of fastphase was slightly higher than with beagle for all traits except number of days to budding and apical length (). to compare the gwas with the genomic prediction results, we ranked the marker […]

2016
PMCID: 4982113
PMID: 27515508
DOI: 10.1186/s12864-016-2918-5

[…] calls were removed. a total of 19,303 polymorphic markers, including 11,126 with minor allele frequencies (maf) ≥ 5 %, were included in the association analyses. missing genotypes were imputed with fastphase []. a genome-wide estimation of ld decay in euchromatic and heterochromatic regions was plotted as physical distance (kbp) vs r2. population structure was examined using the software […]


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fastPHASE in publications

 (271)
PMCID: 5918591
PMID: 29695245
DOI: 10.1186/s12864-018-4690-1

[…] 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. […]

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

[…] 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., we performed a whole-genome sequencing of a lemp-affected leonberger. briefly, we prepared a fragment library […]

PMCID: 5952923
PMID: 29608725
DOI: 10.1093/gbe/evy052

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]


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

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