Table Of ContentsΒΆ
- Overview
- RTG Command Reference
- Command line interface (CLI)
- RTG command syntax
- Data Formatting Commands
- Read Mapping Commands
- Protein Search Commands
- Assembly Commands
- Variant Detection Commands
- Metagenomics Commands
- Pipeline Commands
- Simulation Commands
- Utility Commands
- bgzip
- index
- extract
- aview
- sdfstats
- sdfsplit
- sdfsubset
- sdfsubseq
- sam2bam
- sammerge
- samstats
- samrename
- mapxrename
- chrstats
- mendelian
- vcfannotate
- vcfdecompose
- vcfeval
- vcffilter
- vcfmerge
- vcfsplit
- vcfstats
- vcfsubset
- vcf2rocplot
- svdecompose
- bndeval
- pedfilter
- pedstats
- avrstats
- rocplot
- hashdist
- ncbi2tax
- taxfilter
- taxstats
- usageserver
- version
- license
- help
- RTG product usage - baseline progressions
- Human read mapping and sequence variant detection
- Task 1 - Format reference data
- Task 2 - Prepare sex/pedigree information
- Task 3 - Format read data
- Task 4 - Map reads to the reference genome
- Task 5 - View and evaluate mapping performance
- Task 6 - Generate and review coverage information
- Task 7 - Call sequence variants (single sample)
- Task 8 - Call sequence variants (single family)
- Task 9 - Call population sequence variants
- Create and use population priors in variant calling
- Somatic variant detection in cancer
- AVR scoring using HAPMAP for model building
- RTG structural variant detection
- Ion Torrent bacterial mapping and sequence variant detection
- RTG contaminant filtering
- RTG translated protein searching
- RTG species frequency estimation
- RTG sample similarity
- Human read mapping and sequence variant detection
- Administration & Capacity Planning
- Appendix
- RTG gapped alignment technical description
- Using SAM/BAM Read Groups in RTG map
- RTG reference file format
- RTG taxonomic reference file format
- Pedigree PED input file format
- Genetic map directory
- RTG commands using indexed input files
- RTG output results file descriptions
- SAM/BAM file extensions (RTG map command output)
- SAM/BAM file extensions (RTG cgmap command output)
- Small-variant VCF output file description
- Regions BED output file description
- SV command output file descriptions
- Discord command output file descriptions
- Coverage command output file descriptions
- Mapx and mapp output file description
- Species results file description
- Similarity results file descriptions
- RTG JavaScript filtering API
- Parallel processing approach
- Distribution Contents
- README.txt
- Notice