Comments (5)
If the subgenomes contain homologous chromosomes with each other, it would probably make more sense to build graphs for those chromosomes all together. Otherwise, you can create a lot of mapping ambiguity between sequences that are shared between the homologs.
from vg.
I would like to ask about merging vcf files from the results of minigraph and then filtering for SNP variants (excluding variants larger than 50bp). After that, I plan to process the population data using pangenie and use the population's vcf for the graph transcriptome workflow. I'm not sure if this is the correct approach. How effective is pangenie software for handling small SNP variations? Are there any recommended short genotyper software for SNPs?
from vg.
@glennhickey might know better, but I believe PanGenie does not genotype any small variants. In humans, our collaborators have achieved very good SNP accuracy by projecting graph alignments to a reference with vg surject
and then using DeepVariant. I'm unsure if the DeepVariant pipelines can handle non-diploid genomes though. We also have experimental features to call SNPs on non-reference sequences.
from vg.
PanGenie is pretty good for SNPs, but DeepVariant does much better on GIAB benchmarks. I don't think either works on non-diploid genomes, though.
For PanGenie, I think you're better off filtering SVs after genotyping instead of before.
Please avoid using #4113 for the time being.
from vg.
@glennhickey Thanks. If a polyploid plant is an allopolyploid formed by the hybridization of two species, would it also face the same issues? The chromosome numbers of the two species are inconsistent, and only a small portion of their genetic material is homologous.
from vg.
Related Issues (20)
- Giraffe alignment is very slow and produces warning[vg::Watchdog] messages unless rescue is disabled HOT 13
- Giraffe needs to better deal with systems where multiple processes opening the distance index causes slowdowns
- Any option like BWA MEM '-C'? HOT 1
- vg convert failes while converting gbz to xg with signal 6 error HOT 8
- Release vg v1.60.0
- `vg convert --vg-algorithm` loses start coordinates of paths in its W lines HOT 3
- The Amazing Uninjectable SAM HOT 1
- Throw an error "error: trying to access a snarl tree node of the wrong type" in `haplotypes` HOT 11
- Get input file error HOT 5
- vg pack error
- Negative or "*" end-position for named-coordinates gaf with giraffe HOT 1
- vg autoindex vg giraffe pggb gfa HOT 1
- Hi, I have a question about vg augment. HOT 5
- sdsl-lite cmake issue HOT 3
- Error when trying to map reads to a spliced-pangenome HOT 8
- Different BAM alignments when using an Ubuntu 20.04 base image versus a 22.04 base image
- Issue Converting PGGB GFA Files for Panacus HOT 4
- confused about the number of genome and gff files being provided to vg autoindex while mapping RNA data HOT 3
- Hello, I have a question about vg map. HOT 1
- Update vg rna to project reasonably onto haplotypes containing CNVs
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 vg.