gnomad

This package contains a number of Hail utility functions and scripts for the gnomAD project and the Translational Genomics Group.

Contents

• Getting Started
• Examples
  • Variant Effect Predictor (VEP)
• API Reference
  • sample_qc
    • ancestry
    • filtering
    • pipeline
    • platform
    • relatedness
    • sex
  • utils
    • annotations
    • constraint
    • file_utils
    • filtering
    • gen_stats
    • intervals
    • liftover
    • parse
    • plotting
    • reference_genome
    • release
    • slack
    • sparse_mt
    • transcript_annotation
    • vcf
    • vep
  • resources
    • config
    • grch37
    • grch38
    • import_resources
    • resource_utils
  • assessment
    • parse_validity_logs
    • summary_stats
    • validity_checks
  • variant_qc
    • evaluation
    • ld
    • pipeline
    • random_forest
    • training
• Resource Sources
  • Custom Sources
  • Environment Configuration
• Change Log