Installation
Documentation
- Key concepts
  - Variants
- Tutorials
- Help
- Vtools commands
  - init
  - Import
  - update
  - phenotype
  - lifttover
  - show
  - use
  - select
  - exclude
  - compare
  - associate
  - output
  - export
  - remove
  - execute
  - admin
- Functions
  - ref_sequence
  - mut_sequence
  - track
  - genotype
  - samples
  - in_table
  - other functions
- Vtools report
- Customization
  - Simulation
    - Customized
    - Models
      - Peng2014_ex1
      - Peng2014_ex2
  - Format
    - Formats
      - basic
      - csv
      - plink
      - rsname
      - cumtomized
      - tped
      - map
      - ANNNOVAR
      - CGA
      - CASAVA18Snps
      - CASAVA18Indels
      - functor
      - ANNNOVAR variants
      - ANNNOVAR variants
- Utilities
  - report progress
  - md5sumd
Application
- Annotation
  - Tutorial
  - Customized
  - Genes
  - Variants
    - COSMIC
    - dbNSFP
    - dbSNP
    - Rutgers map
    - database
    - ESP
    - gwasCatalog
    - hapmap
    - thousandGenomes
    - EBI
  - Regions
  - Misc
- Discovery
- Association
Development
- ChangeLog
- Get involved
Administration
- Autolink
Under development
- FAQ

More

Github repo
ScriptOfScripts
bpeng@mdanderson.org

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running R programs
programming in VAT