Welcome to snipar’s documentation!

Contents:

• Guide
  • Introduction
  • Installation
  • Workflow
• Tutorial
  • Test data
  • Inferring IBD between siblings
  • Imputing missing parental genotypes
  • Family-based GWAS with imputed parental genotypes
  • Family-based GWAS without imputed parental genotypes
  • Correlations between effects
  • Polygenic score analyses
• Input files
  • IDs
  • Observed genotypes
  • Pedigree
  • kinship file
  • agesex file
  • phenotype file
  • covariate file
  • genetic relationship (GRM) file
  • weights file
• Output files
  • IBD segments file
  • imputed parental genotypes file
  • text summary statistics
  • HDF5 summary statistics
  • PGS file
  • PGS effects
  • PGS effects sampling covariance
• Command Line Scripts
  • ibd.py
  • impute.py
  • gwas.py
  • pgs.py
  • correlate.py
  • simulate.py
• Simulation Exercise
  • Simulating data
  • Family-based GWAS without imputed parental genotypes
  • Inferring IBD between siblings
  • Imputing missing parental genotypes
  • Family-based GWAS with imputed parental genotypes
  • Increasing power for family-GWAS by including singletons
  • Polygenic score analyses
  • Adjusting indirect genetic effect estimates for assortative mating

Indices and tables

• Index

• Module Index

• Search Page