simGL

simGL simulates genotype likelihoods (GLs) from haplotypic genotype matrices, given information about per-sample coverage and sequencing error rates. It is designed to work seamlessly with the output of tskit and msprime in Python pipelines, but can be used with any haplotypic genotype matrix.

Contents

• Installation
  • Requirements
  • From PyPI
  • From source (development)
  • Running the tests
• Quickstart
  • Simulate a tree sequence
  • Get reference and alternative alleles
  • Simulate read counts
  • Compute genotype likelihoods (GL)
  • Subset to biallelic GLs and write a VCF
• User Guide
  • Genotype matrix requirements
  • Coverage model
  • Genotype likelihood computation
  • Subsetting to biallelic genotypes
  • Normalization
  • Minor-allele frequency estimation
  • Writing a VCF file
  • Writing a pileup file
  • Monomorphic sites
• Background and Theory
  • Coverage simulation
  • Read simulation
  • Genotype likelihoods
  • Minor allele frequency estimation
• API Reference
  • simGL
• Citation
  • Software
  • Methodological references
• Changelog
  • 0.2.0 (unreleased)
  • 0.1.0

Indices and tables

• Index

• Module Index

• Search Page