Comments (3)
It seems related to the data, it slows down at the chr13 range when running without the -t
parameter.
from octopus.
Hi, thanks for your question. This is likely because this region is 'complex' in some way; either there is substantial true or false variation (e.g. due to miss-mapped reads or sequencing errors). It's also possible that the depth is very high in this region. The runtime of Octopus is mostly influenced by the number of candidate haplotypes that are considered, and therefore the number of proximate candidate variants. This particularly affects the cancer calling model as this is considerably more complex than other models, even more-so without a normal sample as there is generally greater uncertainty in sample genotypes.
Unless you have a strong reason to believe that these regions do not contain true variation, in which case you could skip them (e.g. using the --skip-regions
or --skip-regions-file
option), then I wouldn't take any further action. If the runtime is prohibitively long then you could consider ways to reduce runtime (e.g. reducing --max-haplotypes
, --max-somatic-haplotypes
, or --max-genotypes
), although this will likely come at an accuracy cost.
from octopus.
Thanks, @dancooke. We actually looking at variants at these locations (BRCA1 and 2, mostly) and from a visual inspection there's seem to be quite a lot of insertions in this area, that might be increasing complexity. This is IonTorrent data which is know to have lower quality than Illumina, which we are testing soon.
Thanks again.
from octopus.
Related Issues (20)
- Remove depreciated inheritance of std::unary_function
- Call in high heterozygotes
- VCF file is empty
- info on UL nanpore reads HOT 2
- Forest file is still not available for donwloading "std::bad_alloc Error" HOT 9
- Population-level variant calling using accessions with complex ploidy level
- Will octopus add a mode using paired information to compose a linked debruijn graph?
- Can octopus add a feature to add supported read query names of the variants in the INFO field of the output VCF file? HOT 1
- Position of maternal or paternal haplotypes in Octopus after performing TRIO analyses HOT 1
- Models for NovaseqX?
- Encountered an exception during calling 'std::bad_alloc' HOT 2
- training data & regions of the genome used for somatic random forest model
- Build failures on `gcc-13`: `option_collation.cpp:1298: error: redundant move in initialization`
- Build fails, is there a singularity? HOT 1
- ERROR in reading reference index. HOT 2
- Starting Call Set Refinement (CSR) filtering provokes RAM overload HOT 2
- Use with Nanopore long reads HOT 2
- After recompiling from source get error 'Phred: negative error [2024-07-15 12:55:12] <EROR> probability -0.000000' HOT 2
- Binaries compiled for AVX-512 cores do not process the whole genome. HOT 2
- Build fails - Source code errors encountered
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from octopus.