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VSEAMS
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VSEAMS

VSEAMS (variant set enrichment analysis using multivariate sampling) is a pipeline tool for the analysis of genes and genomic intervals enrichment in genome-wide association study (GWAS) data. The VSEAMS algorithm computes p-values for a trait using GWAS summary statistics.



VSEAMS

VSEAMS (variant set enrichment analysis using multivariate sampling) is a pipeline tool for the analysis of genes and genomic intervals enrichment in genome-wide association study (GWAS) data. The VSEAMS algorithm computes p-values for a trait using GWAS summary statistics.

Topic

Genetics; Genetic variation; GWAS study; Genomics

Details

  • Operation: Enrichment analysis
  • Input: BED
  • Output: -
  • Software interface: Command-line user interface
  • Language: Perl, R
  • Operating system: Linux; Mac OS X
  • License: GNU GPL v2
    • Cost: Free
  • Version name: -
    • Maturity: Stable
  • Credit: The National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Allergy and Infectious Diseases, National Human Genome Research Institute, National Institute of Child Health and Human Development, the Wellcome Trust.
  • Contact: chris.wallace _at_ cimr.cam.ac.uk
  • Collection: -

Publications

Burren OS, Guo H, Wallace C "VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes." Bioinformatics 2014; 30(23):3342-8 https://doi.org/10.1093/bioinformatics/btu571
PMID: 25170024
PMCID: PMC4296156


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