Octopus User Manual
User Manual:
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Page Count: 42
- Overview
- Introduction
- What’s in this manual?
- Availability
- License and copyright
- Further assistance
- Introduction
- Variant calling
- Hybrid mapping based variant calling
- Haplotype based variant calling
- Local variant phasing
- Installation
- System Requirements
- Hardware
- Required Software
- Optional software
- Downloading
- Building
- Easy install with Python
- Building with CMake
- Debug builds
- Running tests
- Getting started
- Basic usage
- Required arguments
- Optional arguments
- Reporting bugs
- Requesting new features
- Calling models
- Individual
- Population
- Trio
- Cancer
- Polyclone
- Examples
- Calling germline variants in a single sample
- Calling variants in a targeted exome panel
- Ignoring decoy contigs from a whole genome run
- Calling germline variants in a population
- Calling de novo mutations in a trio
- Calling somatic mutations in a tumour-normal pair
- HLA genotyping
- Calling variants in haploid organism
- Running in multithread mode
- Using a configuration file
- Random forest filtering
- Best practices
- Reference selection
- Read mapping
- Read preprocessing
- Variant calling
- Variant call filtering
- Command line reference
- General
- Read pre-processing
- Variant generation
- Haplotype generation
- Calling
- Trio
- Cancer
- POLYCLONE
- Phasing
- Call filtering
- VARIANT FILTERING
- Measure reference
- Threshold filtering
- Random forest filtering
- Training random forests
- Output format
- Performance optimisation
- Execution time
- Memory consumption
- Multithreading
- Variant generation
- Haplotype generation and phasing
- Calling model selection and parametrisation
- Troubleshooting
- Building
- Why are the requirements so strict?
- CMake chooses a bad compiler
- Compilation fails
- Linking fails
- Boost libraries fail to link
- Compilation has lots of #pragma warnings
- Runtime
- Segmentation fault
- Execution is slow
- Execution delays after initialising calling components in threaded mode
- Run hangs in decoy contigs
- Behaviour
- No calls are reported
- Regions are skipped because of too many haplotypes
- A call changes when a different input region is given
- Why doesn’t octopus report genotype likelihoods?
- Why do octopus VCF files contain * and .?
- SNP accuracy improves in fast mode
- Calling performance is worse with assembler
- Contact
- Appendix
- Installing requirements
- OS X
- Ubuntu
- Variant generation
- Haplotype generation
- Phasing
- Glossary