Table Of Contents

• Overview
  • Introduction
  • RTG software description
  • Installation and deployment
    • Quick start instructions
    • License Management
  • Technical assistance and support
• RTG Command Reference
  • Command line interface (CLI)
  • RTG command syntax
  • Data Formatting Commands
    • format
    • sdf2fasta
    • sdf2fastq
    • sdf2sam
    • fastqtrim
    • petrim
  • Simulation Commands
    • genomesim
    • cgsim
    • readsim
    • popsim
    • samplesim
    • denovosim
    • childsim
    • pedsamplesim
    • samplereplay
  • Utility Commands
    • bgzip
    • index
    • extract
    • aview
    • sdfstats
    • sdfsubset
    • sdfsubseq
    • mendelian
    • vcfannotate
    • vcfdecompose
    • vcfeval
    • vcffilter
    • vcfmerge
    • vcfsplit
    • vcfstats
    • vcfsubset
    • vcf2rocplot
    • svdecompose
    • bndeval
    • pedfilter
    • pedstats
    • rocplot
    • version
    • license
    • help
• Administration & Capacity Planning
  • Advanced installation configuration
  • Run-time performance optimization
  • Alternate configurations
  • Exception management - TalkBack and log file
  • Usage logging
    • Single-user, single machine
    • Multi-user or multiple machines
    • Advanced usage configuration
  • Command-line color highlighting
• Appendix
  • RTG reference file format
  • Pedigree PED input file format
  • Genetic map directory
  • RTG commands using indexed input files
  • RTG JavaScript filtering API
    • VCF record field access
    • VCF record modification
    • VCF header modification
    • Testing for overlap with genomic regions
    • Additional information and functions
  • Distribution Contents
  • README.txt
  • Notice