title: SNPpy--database management for SNP data from genome wide association studies.
abstract: BACKGROUND
  We describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS). This system makes it possible to merge study data with HapMap data and merge across studies for meta-analyses, including data filtering based on the values of phenotype and Single-Nucleotide Polymorphism (SNP) data. SNPpy and its dependencies are open source software.
  
  
  RESULTS
  The current version of SNPpy offers utility functions to import genotype and annotation data from two commercial platforms. We use these to import data from two GWAS studies and the HapMap Project. We then export these individual datasets to standard data format files that can be imported into statistical software for downstream analyses.
  
  
  CONCLUSIONS
  By leveraging the power of relational databases, SNPpy offers integrated management and manipulation of genotype and phenotype data from GWAS studies. The analysis of these studies requires merging across GWAS datasets as well as patient and marker selection. To this end, SNPpy enables the user to filter the data and output the results as standardized GWAS file formats. It does low level and flexible data validation, including validation of patient data. SNPpy is a practical and extensible solution for investigators who seek to deploy central management of their GWAS data.
authors: Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America. faheem@faheem.info
authors: Faheem
authors: F
authors: Mitha
authors: Herodotos
authors: H
authors: Herodotou
authors: Nedyalko
authors: N
authors: Borisov
authors: Chen
authors: C
authors: Jiang
authors: Josh
authors: J
authors: Yoder
authors: Kouros
authors: K
authors: Owzar
mesh_terms: D030541:Databases, Genetic; D055106:Genome-Wide Association Study; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012984:Software