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RFMix specifications


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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  • person_outline Brian K. Maples <>

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RFMix citations


Strong selection during the last millennium for African ancestry in the admixed population of Madagascar

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, […]


Joint ancestry and association test indicate two distinct pathogenic pathways involved in classical dengue fever and dengue shock syndrome

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) […]


Admixture mapping in the Hispanic Community Health Study/Study of Latinos reveals regions of genetic associations with blood pressure traits

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, […]


A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín

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 […]


Selective breeding and selection mapping using a novel wild derived heterogeneous stock of mice revealed two closely linked loci for tameness

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 […]


The time and place of European admixture in Ashkenazi Jewish history

PMCID: 5380316
PMID: 28376121
DOI: 10.1371/journal.pgen.1006644

[…] “sub-genomes” can be independently localized., we begin our analysis by testing the ability of available lai software to correctly infer ancestries for simulated eu/me genomes. proceeding with rfmix, we apply lai to ashkenazi snp array data, and use a maximum likelihood approach to localize, separately, the eu and me sources. we correct bias introduced by the method using simulations, […]

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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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