ND Genotype: Available Documentation

This module provides support and visualization of genotypic data stored in a modified GMOD Chado schema. The 3.x branch of this module represents a shift towards support for large scale genotypic datasets through backwards compatible improvements to the Chado schema including a new gathering table for genotypes (genotype_call) modelled after the chado phenotype table, optimized queries and well-choosen indexes.

Note

Easy Data loading is available via the Genotypes Loader which supports VCF files!

Resources:

• Features
  • Genotype Matrix
  • Marker/Variant Genotype Summary Fields
  • Marker/Variant Flanking Sequence Field
  • Genotype Matrix Quick Link
• Installation
  • Quickstart
  • Dependencies
  • Installation
• Configuration
  • Set Controlled Vocabulary Terms
  • Add Genotype Summaries to Variant/Marker Pages
  • Set Preferred Allele Colours (Optional)
• Use Cases
  • Find a variant in a trait-implicated region
• Data Storage
  • Chado Schema and Extensions
  • Example Database
• Contributing
  • Automated Testing
  • Manual Testing (Demonstration)