Alpha release of octopus

[Daniel Cooke]

Dear all,

I’m very excited to tell you about a new variant calling tool we’ve been developing over the last couple of years. Octopus is a successor to Platypus, and has many fundamental improvements that we believe make it the most advanced variant caller currently available, these include:

• Supports germline, trio and cancer models for calling germline, de novo, and somatic mutations respectively.

• Complex variant calling: like Platypus, octopus has a built in assembler which can result in very large indels being called (over 2,000bp in some cases!).
• Phased calls: octopus outputs phased variant calls by default, and is able to produce very long haplotypes in some instances (e.g. whole HLA genes!). These calls have an associated phase quality.
• Easy performance configuration: by default calling is geared towards accuracy with similar runtimes to GATK, but an optional fast mode improves runtimes to Platypus levels, with only minor calling accuracy penalties. 
• Variable ploidy assumptions.
• Built in multithreading.
• BAM and CRAM support.
• Output directly to compressed VCF or BCF.
• Consistent VCF output: overlapping calls are handled in a consistent manner.

To give an idea of calling accuracy compared to existing tools, here are some results using the latest Genome in a Bottle NA12878 high confidence reference set (SNPs + indels).

These results were made using each caller's recommended settings and default output (Platypus: outputs filtered calls by default. GATK: as per best practice instructions, only calls with quality above 30 were considered; no VQRS filtering was applied. Samtools: reaches good sensitivity but only at high FP rates; not shown on graph). Variants were compared using the latest version of RTG Tools.

We will release performance figures for the somatic and de novo callers in due course, and papers should follow.

The source code is available on Github. It is written in C++ and has been carefully designed and tested. Extensive documentation is available online, and users can expect prompt support and response to feedback.

Octopus is currently in alpha release. It may be unstable, it is not feature complete, may contain bugs etc. We are making it available at this stage to give potential users the chance to get a feel for how it works and give feedback.

Best wishes,

Daniel

[Sirisha Hesketh]

Hi Dan,

We're interested in giving Octopus a go, but the github link seems to be broken - any update on when this will be available again?

Thanks,
Sirisha

[Duarte Molha]

Where is it?

After such amazing introduction to it I would like to test it... even in alpha... but link does not exist

[ni...@cc-tdi.org]

Was this project abandoned?

[Daniel Cooke]

Dear all,

I’m pleased to announce that Octopus is back online, for good! We’ve made a number of improvements over the last year, in particular, de novo and somatic mutation calling is much improved.

Best of all, we now have a logo!

The project is still hosted on Github.

Best wishes,

Dan

On 3 Aug 2017, at 09:16, Gerton Lunter <gerton...@well.ox.ac.uk> wrote:

Dear Nick,

No, it’s still under development.  We had to pull it temporarily because of IP issues, but we aim to get it back online as soon as possible.

Best wishes

Gerton