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
• Hail Query and Batch
  • Query
  • Batch
• Pre-Imputation QC
  • Arguments and options
  • Output(s)
  • Examples
• Principal Component Analysis
  • Normal PCA
  • Joint PCA
  • Projection PCA
  • Arguments and options
  • Output
• Haplotype Phasing
  • Examples
  • Arguments and options
  • Output
• Genotype Imputation
  • Examples
  • Arguments and options
  • Output
• Tutorial
  • 1. Datasets
  • 2. Start a dataproc cluster with GWASpy installed
  • 3. Pre-imputation QC
  • 4. PCA
  • 5. Phasing and Imputation
  • 6. Low-coverage WGS imputation using GLIMPSE