Comments (5)
Hi Melissa,
What did SURVIVOR tell about the error?
Yekai
from duet.
Hi Yekai,
There's no error message. It lists the number of entries in both files but doesn't merge them. I tried two Duet vcfs, a Duet vcf and an unphased cutesv vcf, and a duet vcf and a short-read vcf. It's the same issue with all of them.
I'm using very relaxed parameters but when I relax them further by reducing the minimum number of supporting callers from 2 to 1, I don't get any calls made in both samples even though they are a mother child pair.
Melissa
from duet.
I think maybe it is because Duet is outputting phased SV sets with the format of "0|1", "1|0", and "1|1". The other SV callers output pre-phased calls in the format of "0/1" and "1/1".
Could you please try replacing "0|1" and "1|0" to "0/1", and "1|1" to "1/1" in Duet output, and then try using survivor to combine/compare the output with other SV callers?
Yekai
from duet.
I tried and it doesn't help. I don't think this would be an issue since I've used survivor on phased linked-reads that use a combination of 0/1 and 0|1 notation without a problem.
from duet.
Dear Melissa,
I suggest you to report an issue to SURVIVOR with your case and some head lines of the SV calls to see if they can give some suggestions. I am not familiar with the design of SURVIVOR and maybe they can tell you where the incompatibility is, and then we can fix out how to modify the Duet vcf.
Yekai
from duet.
Related Issues (13)
- Feature request: control for clair3 parameters HOT 4
- Increase support for species with. different number of chromosome HOT 2
- pinned bcftools version libcrypto.so.1.0.0: issue HOT 4
- [Enhancement] Sniffles as extra sv_caller HOT 3
- SNP phasing not running HOT 6
- Feature enhancement: ability to provide sample name for VCF HOT 1
- error when run the duet demo data HOT 6
- Could not load dynamic library 'libcudart.so.11.0'; dlerror: HOT 2
- SNP calling not working HOT 6
- bug: np.int() no longer exists. HOT 6
- Request: A docker image with duet HOT 3
- Combining calls from multiple samples
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 duet.