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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

Versioning


No version available

Maintainer


  • person_outline Matti Pirinen

Publication for FINEMAP

FINEMAP citations

 (6)
library_books

A whole genome sequence study identifies genetic risk factors for neuromyelitis optica

2018
Nat Commun
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) The associati […]

library_books

Trans ethnic meta regression of genome wide association studies accounting for ancestry increases power for discovery and improves fine mapping resolution

2017
Hum Mol Genet
PMCID: 5755684
PMID: 28911207
DOI: 10.1093/hmg/ddx280

[…] een 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 and F […]

library_books

Constraints on eQTL Fine Mapping in the Presence of Multisite Local Regulation of Gene Expression

2017
PMCID: 5555460
PMID: 28600440
DOI: 10.1534/g3.117.043752

[…] effects. Two exhaustive search algorithms, PAINTOR () and CAVIARBF (), hold promise for detailed dissection of multisite models at individual loci, and a Bayesian shotgun stochastic search algorithm, FINEMAP (), has recently been proposed for rapid maximum likelihood estimation of multi-SNP contributions. Here, we show by simulation that DAP () does indeed improve on sequential conditional analysi […]

library_books

JAM: A Scalable Bayesian Framework for Joint Analysis of Marginal SNP Effects

2016
Genet Epidemiol
PMCID: 4817278
PMID: 27027514
DOI: 10.1002/gepi.21953

[…] ft y‐axis), as well as the power/sensitivity (right y‐axis), over a range of rank thresholds, and averaged over 200 simulation replicates. The sparse Bayesian regression approaches (JAM, CAVIARBF and FINEMAP) all performed very similarly, offering near perfect discrimination of the three signal SNPs. They all outperformed COJO's stepwise search. As a proof of principle and for the sake of comparis […]

library_books

Dense genotyping of immune related susceptibility loci reveals new insights into the genetics of psoriatic arthritis

2015
Nat Commun
PMCID: 4327416
PMID: 25651891
DOI: 10.1038/ncomms7046

[…] e applied a Bayesian refinement approach to define the subset of SNPs that, based on posterior probability, is 99% likely to contain the causal disease-associated SNP (https://github.com/chr1swallace/finemap-psa). These credible SNP sets were then annotated for putative function based on transcript location (refseq gene annotation) and localization to ENCODE features (H3K4Me1, H3K4Me3, H3K27Ac, DN […]

library_books

Exploring the 7p22.1 Chromosome as a Candidate Region for Autism

2010
PMCID: 2856063
PMID: 20414355
DOI: 10.1155/2010/423894

[…] t(7;16) translocation, showed that the chromosomal rearrangement implicates the chromosomes 7 and 16 only, and established that the translocation is reciprocal and apparently balanced ().In order to finemap the breakpoint on 7p22.1, we performed FISH using BAC End clones from this chromosomal region as probes. BAC DNAs (RPCI-11 library) were biotinylated with biotin-11-dUTP (Sigma) by nick transl […]


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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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