VariantGrid Docs

VariantGrid is a source available variant database and web application for analyzing genetic data.

This documentation is intended for users. There are also Admin docs and Developers Technical Wiki

Overview:

• Intro
  • Cloud servers
  • Private server
• Technical Attributions
  • Genetic/Medical Databases

Analysis:

• Analysis Intro
  • Analysis Nodes
  • Analysis screen
  • Analysis Grid
• Analysis Nodes
  • Source Nodes
  • Filter Nodes
• Analysis - advanced
  • Analysis settings
  • Node Counts
  • Column Summary
• Variant Tagging
  • Create tags
  • Tagging variants
  • Using tags
• Analysis Classification
• Analysis - templates
  • Overview
  • Running Analysis templates
  • Creating Analysis Templates
• Karyomapping
  • Background
  • Gene analysis
  • Genome-wide analysis

Annotations:

• Annotation Details
  • Variant Level Annotation
  • Annotation Versions
• Variant Details
  • Classifications
  • Transcripts
  • Samples
• Transcript Choice
  • Analysis transcripts
  • Representative Transcript

Data:

• Uploading Data
• Managing data
  • Sharing data
• Somatic data
  • Allele Frequency
• Mutational signatures
• VCF / Samples
  • VCF import
  • Multi-sample VCFs
  • VCF Normalization
• Relatedness
  • VCF relatedness
  • Sample relatedness
• Ancestry
  • Implementation details
• Search
• Zygosity counts
  • Global Counts
  • VCF configuration

Genes:

• Genes
  • Genes and symbols
  • RefSeq vs Ensembl
  • Gene Annotation Release
  • Gene Annotation Grid
• Gene Symbol page
  • Gene Annotation
  • Internal gene data
• Gene Lists
  • Creating Gene Lists
  • Using gene lists in an analysis
• Gene Grid
  • GeneGrid screen
  • Gene Info
• Gene Coverage
  • Canonical Transcripts
  • Sample QC metrics
  • GeneGrid EnrichmentKit coverage

Path Tests:

• Pathology Tests
  • Active tests
  • Requesting gene changes
  • Accepting gene changes
• Test Ordering

Patients:

• Patients
  • Searching
  • Patient records
  • Other sources of patients
  • Other
• Phenotypes
  • Assigning Terms to Patients
  • How phenotype term matching works
• Cohorts
  • Create a new cohort
  • Create from a larger cohort
  • Cohort Analyses
• Trios
  • Creating a trio
  • Digital karyomapping
  • Trio inheritance analysis
• Pedigree

Sequencing:

• Sequencing Runs
  • Enrichment Kit
  • Gold Standard Runs
  • Finding sequencing data
  • Triggering a manual scan

Settings:

• User Details
  • Groups
  • Initial group permissions
  • Node counts
  • User Settings
• Customise columns
  • Changing columns
  • Default columns
  • Changing columns in an analysis
• IGV integration
  • IGV Configuration
  • VariantGrid Configuration
  • Network drives and File Servers

Classification:

• Classifications
  • Creating Classifications
  • Create from existing variant
  • Editing
  • Configuring Fields
• Classification Form
  • View
  • Identify Errors
  • Change History / Diff
  • ACMG Guidelines
  • Actions
  • Export
  • Literature Citations
• Classification Sharing
  • How to share
  • External systems
  • Private fields
  • Withdraw
• Classification Flags
  • Flag Dialog
  • Flag Types
• Classification Report
  • Running the report
  • Configuring the report
• Classification REDCap
  • REDCap Definition
  • REDCap Rows
  • Technical Specifics

Indices and tables

• Index

• Module Index

• Search Page