User: daniel
daniel • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- United Kingdom
- Last seen:
- 5 months, 2 weeks ago
- Joined:
- 5 years, 6 months ago
- Email:
- d*****@well.ox.ac.uk
I'm a DPhil student at Oxford University.
Posts by daniel
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... [Octopus](https://github.com/luntergroup/octopus) is capable of tumour only somatic and germline variant calling. There is an evaluation of tumour-only calling on WGS data in the [Octopus paper](https://www.biorxiv.org/content/early/2018/10/29/456103). ...
written 2.7 years ago by
daniel • 30
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... Octopus is back online - the link should now work. ...
written 2.8 years ago by
daniel • 30
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... Octopus is now back online - the link should now work. ...
written 2.8 years ago by
daniel • 30
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... I've recently developed a C++ library, [Mappable](https://github.com/dancooke/mappable), which efficiently handles intervals. It allows you to write stuff like this:
std::vector mappables {};
/* insert data */
const auto overlapped = overlap_range(mappables, some_interval); // returns a ...
written 2.8 years ago by
daniel • 30
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... To expand Zam's answer, we have just released an alpha version of Platypus' successor, [octopus](https://github.com/luntergroup/octopus). By default octopus isn't much faster than GATK, but it does have an optional fast mode which gives similar runtimes to Platypus with little loss in calling accura ...
written 3.9 years ago by
daniel • 30
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... Just thought I'd shamelessly give our new haplotype-based variant caller [octopus](https://github.com/luntergroup/octopus) a mention here. It has a built in trio model that is able to classify called variants as de novo. There is no need for read pre-processing or messy post-hoc VCF intersections. C ...
written 3.9 years ago by
daniel • 30
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... Just thought I'd give my C++ library, [Bioio][1], a mention here. Although primarily a C++ API for FASTA/Q I/O, I also include a small command line application demo fasta.cpp which can be used to retrieve indexed FASTA subsequences, e.g.
./fasta human_g1k_v37.fasta X:10000-20000
Like samtools, ...
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