RFMix protocols

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RFMix specifications

Information


Unique identifier OMICS_12589
Name RFMix
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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Maintainer


  • person_outline Brian K. Maples <>

Publication for RFMix

RFMix in pipeline

2017
PMCID: 5344536
PMID: 28241052
DOI: 10.1371/journal.ppat.1006220

[…] analyses were carried out in plink [] through the χ2 statistics. p-values were displayed as–log10 in manhattan plots, obtained in haploview., local ancestry analysis was performed through rfmix algorithm []. 50 southern european (italian) and 50 yoruban samples from the 1000 genomes database [] represented the parental european and african components, respectively. these samples […]


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RFMix in publications

 (28)
PMCID: 5834599
PMID: 29500350
DOI: 10.1038/s41467-018-03342-5

[…] vs. chinese from bejing; (b) esan vs. mandar; (c) luhya vs. mandar; and (d) yoruba vs. mandar. a third analysis was performed using the same pool of individuals as in the first analysis, but using rfmix instead of elai to assign the local ancestry; the data were first phased with beagle version 4.1. rfmix was run twice, first with the popphased option selected in the command, […]

PMCID: 5813895
PMID: 29447178
DOI: 10.1371/journal.pntd.0006202

[…] (dss test); and vietnamese dss versus controls (dss test). samples were phased in shapeit v.2 [] using hapmap reference panel and fine-scale genetic map., for admixture mapping, we applied the rfmix algorithm [] and used three ancestral data sets: the phased data from the 1,000 genomes database [] for the chinese dai in xishuangbanna (cdx); and the indian telugu from the uk (itu) […]

PMCID: 5695820
PMID: 29155883
DOI: 10.1371/journal.pone.0188400

[…] as pc plots and additional information about the construction of the groupings are provided in []., local ancestry inference has been reported in browning et al. (2016) []. it was performed using rfmix [] based on the genotyping values and a reference panel derived from the human genome diversity project [] (hgdp) and the 1000 genome project []. this resulted in 14,815 intervals, […]

PMCID: 5633392
PMID: 28855283
DOI: 10.1534/g3.117.1118

[…] american populations were inferred from the pruned snp set using admixture with k = 3 ancestral populations, using the african, european, and native american reference populations shown in . the rfmix program (), version 1.5.4, was used for both local ancestry inference and to obtain a corresponding set of rephased genotypes. rfmix was run in the popphased mode with a minimum node size […]

PMCID: 5496859
PMID: 28676693
DOI: 10.1038/s41598-017-04869-1

[…] of subsequent analyses. finally, we obtained data on 52,135 snps of 128 whs mice and eight founder strains (table )., to infer the haplotypes of whs founder strains, we used beagle v. 4.0 and rfmix v. 1.5.4, a program for local-ancestry inference that uses a discriminative approach with a conditional random field parameterized by random forest. the program was trained to distinguish […]


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RFMix institution(s)
Department of Genetics, Stanford University, Stanford, CA, USA; Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA; Department of Human Genetics, McGill University, Montreal, QC, Canada; Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center of Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sanai, New York, NY, USA
RFMix funding source(s)
This work was supported by National Science Foundation (NSF) Graduate Research Fellowship grant DGE-1147470, National Library of Medicine training grant LM007033, National Human Genome Research Institute grant 2R01HG003229, and NSF Division of Mathematical Sciences grant 1201234.

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