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Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time.

There are currently six calling models available:

- [individual](https://luntergroup.github.io/octopus/docs/guides/models/individual): call germline variants in a single healthy individual.
- [population](https://luntergroup.github.io/octopus/docs/guides/models/population): jointly call germline variants in small cohorts.
- [trio](https://luntergroup.github.io/octopus/docs/guides/models/trio): call germline and _de novo_ mutations in a parent-offspring trio.
- [cancer](https://luntergroup.github.io/octopus/docs/guides/models/cancer): call germline and somatic mutations tumour samples.
- [polyclone](https://luntergroup.github.io/octopus/docs/guides/models/polyclone): call variants in samples with an unknown mixture of haploid clones, such a bacteria or viral samples.
- [cell](https://luntergroup.github.io/octopus/docs/guides/models/cell): call variants in a set of single cell samples from the same individual.

Octopus calls SNVs, small-medium sized indels, and small complex rearrangements in [VCF 4.3](https://luntergroup.github.io/octopus/docs/guides/advanced/vcf).

## Quick start

Install Octopus:

```shell
$ git clone https://github.com/luntergroup/octopus.git
$ octopus/scripts/install.py --dependencies --forests
$ echo 'export PATH='$(pwd)'/octopus/bin:$PATH' >> ~/.bash_profile
$ source ~/.bash_profile
```

Call some variants:

```shell
$ FOREST="$(pwd)/octopus/resources/forests/germline.v0.7.4.forest"
$ octopus -R hs37d5.fa -I NA12878.bam -T 1 to MT -o NA12878.octopus.vcf.gz --forest $FOREST --threads 8
```

## Documentation

Documentation is hosted on [GitHub pages](https://luntergroup.github.io/octopus/).

## Support

Please report any bugs or feature requests to the [octopus issue tracker](https://github.com/luntergroup/octopus/issues). General chat is hosted on [Gitter](https://gitter.im/octopus-caller/Lobby).

## Contributing

Contributions are very welcome! Please consult the [contribution guidelines](CONTRIBUTING.md).

## Authors

Daniel Cooke and Gerton Lunter

## Citing

See [publications](https://luntergroup.github.io/octopus/docs/publications) associated with Octopus.

## License

Octopus is distributed under the [MIT LICENSE](LICENSE).