Welcome to VAPr’s documentation!

Contents:

• Introduction
  • Installation
    • Ancillary Libraries
    • MongoDB
    • BCFtools
    • Tabix
    • ANNOVAR
    • VAPr
  • Annotation Quickstart using ANNOVAR
    • Downloading the ANNOVAR databases
• Downstream Analysis
  • Filtering Variants
    • 1. Rare Deleterious Variants
    • 2. Known Disease Variants
    • 3. Deleterious Compound Heterozygous Variants
    • 4. De novo Variants
    • Create your own filter
  • Output Files
    • Unfiltered Variants CSV
    • Filtered Variants CSV
    • Unfiltered Variants VCF
    • Filtered Variants VCF
• VAPr core
• Tutorial
• API Reference
  • Submodules
  • VAPr.annovar_output_parsing module
  • VAPr.annovar_running module
  • VAPr.chunk_processing module
  • VAPr.filtering module
  • VAPr.validation module
  • VAPr.vapr_core module
  • VAPr.vcf_genotype_fields_parsing module
  • VAPr.vcf_merging module
  • Module contents

Indices and tables

• Index
• Module Index
• Search Page