User: daniel

gravatar for daniel
daniel30
Reputation:
30
Status:
New User
Location:
United Kingdom
Last seen:
7 months, 4 weeks ago
Joined:
4 years, 9 months ago
Email:
d*****@well.ox.ac.uk

I'm a DPhil student at Oxford University.

Posts by daniel

<prev • 7 results • page 1 of 1 • next >
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Answer: A: single sample somatic variant calling software
... [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 2.0 years ago by daniel30
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Comment: C: Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
... Octopus is back online - the link should now work. ...
written 2.0 years ago by daniel30
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Comment: C: Identifying De Novo Variants In Trio Data
... Octopus is now back online - the link should now work. ...
written 2.0 years ago by daniel30
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Answer: A: Fast Interval Intersection Methodologies
... 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 2.0 years ago by daniel30
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Answer: A: Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
... 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 3.1 years ago by daniel30
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Answer: A: Identifying De Novo Variants In Trio Data
... 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 3.1 years ago by daniel30
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Answer: A: Extract User Defined Region From An Fasta File
... 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, ...
written 4.2 years ago by daniel30 • updated 11 weeks ago by RamRS24k

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