fastPHASE pipeline

fastPHASE specifications


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

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 [108]. 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 […]

PMCID: 4468903
PMID: 26040272
DOI: 10.1038/ncomms8330

[…] on the ensembl gene annotation of the collared flycatcher reference genome version ficalb1.4, as well as regions with >20% sites hard-masked by repeatmasker. we phased the selected region with fastphase v1.4.0 (ref. 68), using sequence data from 198 flycatcher individuals. to minimize phasing errors, we recoded all heterozygous genotypes with <80% posterior phasing probability […]

PMCID: 3656791
PMID: 23663537
DOI: 10.1186/1471-2156-14-41

[…] 5% significance threshold corresponds to 2.5 × 10-5., haploview 4.2 [35] was used to analyze the linkage disequilibrium among the snps. the diplotypes of the gwas samples were estimated using fastphase 1.2 software [36] and beagle 3.3.2 software [37,38]., the genotypes of 33,303 snps were imputed using beagle 3.3.2 software [37,38], with haplotype information inferred from 586,812 snps […]

PMCID: 2843742
PMID: 20352120
DOI: 10.1371/journal.pone.0009827

[…] analyses of long range ld using the 104 affymetrix snps covering ∼1 mb region, we first inferred long-range haplotypes using the algorithm by scheet and stephens [31], implemented in the software fastphase.v130.beta (details in supplementary file s1). we tested for the presence of recombination hotspots along the ∼1 mb using the approximate marginal likelihood method by fearnhead [32] […]

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

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