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https://github.com/luntergroup/octopus

Bayesian haplotype-based mutation calling
https://github.com/luntergroup/octopus

bioinformatics de-novo-mutation genomics haplotypes phasing single-cell somatic-variants variant-calling variants

Last synced: 3 months ago
JSON representation

Bayesian haplotype-based mutation calling

Host: GitHub
URL: https://github.com/luntergroup/octopus
Owner: luntergroup
License: mit
Created: 2015-02-04T09:24:53.000Z (almost 10 years ago)
Default Branch: develop
Last Pushed: 2023-08-12T10:33:07.000Z (about 1 year ago)
Last Synced: 2024-06-21T18:24:59.927Z (5 months ago)
Topics: bioinformatics, de-novo-mutation, genomics, haplotypes, phasing, single-cell, somatic-variants, variant-calling, variants
Language: C++
Homepage:
Size: 137 MB
Stars: 298
Watchers: 19
Forks: 37
Open Issues: 46
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE

Awesome Lists containing this project

Awesome-Bioinformatics - Octopus - A polymorphic bayesian genotyping model with wide applicability. [ [paper-2021](https://www.nature.com/articles/s41587-021-00861-3) ] (Next Generation Sequencing / Variant Calling)

README

        ![Octopus Logo](logo.png)

[![Website](https://img.shields.io/website?url=https%3A%2F%2Fluntergroup.github.io%2Foctopus%2F)](https://luntergroup.github.io/octopus/)

[![Build Status](https://travis-ci.org/luntergroup/octopus.svg?branch=master)](https://travis-ci.org/luntergroup/octopus)

[![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)

[![Gitter](https://badges.gitter.im/octopus-caller/Lobby.svg)](https://gitter.im/octopus-caller/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)

![GitHub release (latest SemVer)](https://img.shields.io/github/v/release/luntergroup/octopus)

[![Anaconda-Server Badge](https://anaconda.org/bioconda/octopus/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)

[![Docker Image Version (latest semver)](https://img.shields.io/docker/v/dancooke/octopus?label=docker)](https://hub.docker.com/r/dancooke/octopus)

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).