Comments (2)
Hi @aysegokce,
Thank you for developing HiPhase! I liked how HiPhase handles haplotagging supplementary alignments. Ishttps://github.com//issues/5#issuecomment-1536659101 by default, or should I pass a parameter?
Yes, this is enabled by default. If you want to disable it, you can use the --no-supplemental-joins
option.
Is there a suggested workflow for tumor-normal pairs?
In this context, we only officially support "normal" sample types. Tumor will obviously have a variety of deviations from normal that HiPhase currently does not account for.
We usually run the Clair3 (or DV) + whatshap phase with normal and then use whatshap to haplotag both tumor and normal using the phased vcf. Is there such functionality?
Just to verify, here is the pipeline I think you're describing; please correct any errors:
- Run a variant caller on the normal dataset.
- Phase and haplotag the normal dataset using WhatsHap.
- Use WhatsHap to haplotag the tumor dataset using the phased VCF from the normal dataset.
Assuming the above is correct, HiPhase currently cannot do step 3. This is because the phasing and tagging steps make the assumption that the dataset and parameters are identical. I believe you would be able to perform steps 1 and 2 with HiPhase, and then the final step with WhatsHap. I suspect that most haplotagging would be correct, but there would likely be some corner cases that don't work well.
The use case is interesting, but we built HiPhase under the assumption of a single dataset to phase/haplotag. I'll have to think more about how feasible this is with HiPhase.
Matt
from hiphase.
@holtjma Thank you for the explanation.
Currently, whatshap does not support supplementary alignment phasing. So, it would be nice to have HiPhase work with tumor/normal pairs as well.
Ayse
from hiphase.
Related Issues (20)
- Poor utilization of threads (maybe user error?) HOT 6
- Error βthread '<unnamed>' panicked at 'assertion failed: `(left == right)`β occurred while HIPhase working HOT 7
- segmentation fault (core dumped) HOT 2
- Encountered max_edit_distance check HOT 6
- Recommendations for input vcf HOT 3
- A question about HP tag HOT 6
- reference letter case issue HOT 2
- Feature request: haplotag in phased VCF files HOT 2
- Error while parsing VCF file: FORMAT columns HOT 3
- Expected memory usage HOT 3
- Phase vcf with pre phased reads HOT 6
- Normalization of INDELs: required or should be avoided HOT 3
- [Suggestion] reducing messages to STDOUT to speed up the utility HOT 3
- [Question] information in the filter column of vcfs HOT 2
- [Question] Phasing of rs36056539 in NA19226 HOT 3
- ERROR : 0 matched samples for phasing HOT 2
- possibility to utilize information from phased bam files HOT 4
- thread 'main' panicked error HOT 3
- gVCF + VCF processing HOT 6
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π 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. πππ
-
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 β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hiphase.