MAGMA pipeline

MAGMA specifications

Information


Unique identifier OMICS_10909
Name MAGMA
Alternative name Multi-marker Analysis of GenoMic Annotation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data MAGMA can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Beta
Maintained Yes

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Documentation


Publication for Multi-marker Analysis of GenoMic Annotation

MAGMA IN pipelines

 (3)
2018
PMCID: 5959890
PMID: 29777097
DOI: 10.1038/s41398-018-0150-6

[…] were defined by combining lead snps within a 250 kb window and all snps in ld of at least r2 = 0.6 with one of the independent snps. a gene-based analysis was carried out on all snp output using the magma software15 with default settings (snp-wise (mean) model for each gene), and assuming a constant sample size for all genes. a bonferroni-adjusted p-value of 0.05/18,251 = 2.7 × 10−6 was used […]

2018
PMCID: 5959890
PMID: 29777097
DOI: 10.1038/s41398-018-0150-6

[…] for all genes. a bonferroni-adjusted p-value of 0.05/18,251 = 2.7 × 10−6 was used to identify significant genes. the 1000 genomes phase 3 data16 were used to map ld in both the independent locus and magma analyses., to test for pleiotropic associations between snps and ad and gene expression/dna methylation in the brain, summary data-based mendelian randomisation (smr) was performed17. gwas […]

2016
PMCID: 5147879
PMID: 27936112
DOI: 10.1371/journal.pone.0167388

[…] window to include gene regulatory regions and maf ≥ 0.05. the genes were encoded by ensembl identifiers (release 75, genome assembly h19). pathways were assigned competitive p-values using magma v1.05 [29] which assesses whether a pathway is more associated with a trait than other pathways, and takes into account linkage disequilibrium (ld). the reference data used for ld […]

MAGMA institution(s)
Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands; Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, Netherlands; Informatics Institute, University of Amsterdam, Amsterdam, Netherlands; Department of Clinical Genetics, VU University Medical Centre Amsterdam, Neuroscience Campus Amsterdam, Netherlands
MAGMA funding source(s)
This study was conducted as part of the Complexity project of the Netherlands Scientific Organisation, grant NWO 645-000-003.

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