Comments (4)
There are two ways I'm considering for the read depth:
- We calculate the read depth over the entire BAM file (maybe using a sliding window average), and then use the discrepancies to call breakends. This would occur in the variant detection stage.
- We feed in a vector of clusters for just insertions and deletions (since those are the only two which can be detected via read depth), and can then either support or not support the call. This would occur after the variant detection and clustering stages.
from igenvar.
Since we assume with 1 that our breakpoints are probably very fuzzy, I would prefer version 2.
But we should keep in mind, that there is the possibility of version 1, which we could doublecheck later. Question would be, are there lot of SVs just detected by read depth and how fuzzy are the breakpoints..
In addition to insertions and deletions, there are also duplications (which are basically insertions aswell).
from igenvar.
I would say using just read depth would be not very accurate. But if you use it in combination with the other methods, then the fuzzy breakends don't matter too much since they'll be supported by things like split reads which have much more precision.
from igenvar.
Okay, then I would say we go with version 1 and then see if our F1 score in the benchmarks suffers or benefits. 👍
from igenvar.
Related Issues (20)
- [FEATURE] Extend VCF output with CN (copynumber)
- [BUG] Count duplications in the reference
- How do we track constant parameters?
- [TEST] Do some short read benchmarks
- [FEATURE] Add filedate to VCF header
- [BENCHMARK] Make iGenVar results deterministic
- [MISC] Update seqan3 to get thread problem fixed.
- [DOC] Update doxygen support to 1.9.3
- [FEATURE] Use b.i.o. library for vcf parsing.
- iGenVar - [BENCHMARK] Create short & long read benchmarks
- [BUG] Input files are based on GRCh37 (hg19) others on GRCh38 (hg38)
- [BENCHMARKS] Examine the calling results more closely.
- Dependency managment
- iGenVar - Call Inversions
- [BUG] The commit 91ec8dc "Add iGenVar_SVLEN" brought a bug.
- Recheck TANDEM:DUPs
- [INFRA] Switch to original biocpp-io submodule
- [BENCHMAKRS] Do some simulation benchmarks
- Release 0.1.0
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 igenvar.