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 statistic

SUBMITTER: Mitha F 

PROVIDER: S-EPMC3198468 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature