FINEMAP statistics

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Associated diseases

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FINEMAP specifications

Information


Unique identifier OMICS_11035
Name FINEMAP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Space-delimited input files
Output data FINEMAP outputs a regional Bayes factor on log10 scale to assess the evidence against the N/A model where none of the SNPs are causal.
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Matti Pirinen <>

Publication for FINEMAP

FINEMAP in publications

 (10)
PMCID: 5955905
PMID: 29769526
DOI: 10.1038/s41467-018-04332-3

[…] nmo-igg−, providing a potentially novel biological hypotheses for seropositive nmo pathogenesis related to low c4 expression. given the complexity of the mhc region, larger studies will be needed to finemap and disentangle the role of classical hla alleles to that of c4 structural variation as well as to understand the effect of these haplotypes on the nmo-igg negative subgroup. (3) […]

PMCID: 5621629
PMID: 28869591
DOI: 10.1038/ng.3949

[…] tools to prioritize likely candidate genes and variants. these included the variant effect predictor software to identify deleterious coding variation at genome-wide significant loci (), the finemap software to create configurations of plausible causal snps around each conditionally independent lead snp (), encode maps of dnase i hypersensitivity sites (dhs) , and contextual analysis […]

PMCID: 5755684
PMID: 28911207
DOI: 10.1093/hmg/ddx280

[…] recent development of novel methods for fine-mapping that utilise meta-analysis summary statistics and a reference panel of ld between variants across a locus, including caviar (), paintor () and finemap (). by modelling ld between variants across a locus, these approaches have the advantage that they can allow for fine-mapping of multiple causal variants, simultaneously. however, caviar […]

PMCID: 5555460
PMID: 28600440
DOI: 10.1534/g3.117.043752

[…] utilizing a posterior inclusion probability to choose the causal variant credible interval dap software was then developed () to explore high probability causal intervals with reasonable runtime. finemap () uses logical schema that is similar to that of caviar, but adopts a shotgun stochastic search method to restrict the search space and focus on combinations of high probability intervals., […]

PMCID: 5321433
PMID: 28225770
DOI: 10.1371/journal.pone.0171508

[…] for this cis-element had been proposed previously based on the fact that it was bound by key pancreatic regulators [,,]. within this activating sequence we performed a mutation screen to further finemap the critical bases. notably, two of the mutations that inhibit neurog3 activation were high-affinity binding sites for pdx1, a transcription factor previously shown to be a critical regulator […]


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FINEMAP institution(s)
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; National Institute for Health and Welfare (THL), Helsinki, Finland; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
FINEMAP funding source(s)
This work was financially supported by the Doctoral Programme in Population Health, the Academy of Finland [257654, 288509, 251217, 255847] and a Wellcome Trust Career Development Fellowship [097364/Z/11/Z].

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