GWASpy 0.1

GWASpy is an open-source Python package for scalable: (1) Pre-imputation QC; (2) Principal Component Analysis; (3) Haplotype phasing; and (4) Genotype Imputation. See the installation page to get started using GWASpy.

Contents

• Installation
  • Mac OS X
  • Linux
• Pre-Imputation QC
  • Examples
  • Arguments and options
  • Output(s)
• Principal Component Analysis
  • Normal PCA
  • Joint PCA
  • Projection PCA
  • Arguments and options
  • Output
• Haplotype Phasing
  • A. Run scatter, phase, and concat in a single command
  • B. Run scatter, phasing, and concat steps in separate commands.
  • C. Reference panels
  • Arguments and options
  • Output
• Genotype Imputation
  • A. Run imputation+concat in a single command
  • B. Run imputation and concat in separate commands
  • Arguments and options
  • Output