Comments (7)
Hi there,
Thanks for the opinion. I'm currently using gvcf output from calling ONT reads with clair3, commit merging and perform recalling with gatk. Works fine without any bugs for the 1st run with around 40 individuals.
With my limited knowledge I'm not sure if gvcf improves chance of detecting SNP, but I'm aware that the GATK haplotype calling algo claim that by having variant call record at all sites boosted up the confidence. In our pipeline we also deploy Sniffles2 to detect structural variant, and it support joint calling also, so I believe there are merits in the method π . Just my 2 cents.
Tuan
from nanocaller.
Hi Colin,
Thank you for this suggestion. Currently, NanoCaller only does single sample variant calling. We have started working on expanding variant calling for multiple samples in NanoCaller and hopefully we will have something within the next month or so.
from nanocaller.
Ok, thanks for this, it's good to hear.
from nanocaller.
A bit late to the party, but I'm also interested in this. In our current approach, we attempt to call single sample with Clair3 (with GVCF output). Then do a merge & force recall with GATK. I wonder if the same approach can be deployed with NanoCaller.
from nanocaller.
Hi, yes you can try to do a similar approach with NanoCaller by running NanoCaller on individial samples and merging them with an external tool such as GATK. We have not tested this strategy ourselves but in theory it should work. You can specify sample names in NanoCaller VCF files by using --sample
parameter so that VCF files can be merged.
from nanocaller.
Hi there, thanks for the response,
If that is the case, it is perhaps beneficial for NanoCaller to output gvcf instead of normal vcf, so that all sites can be recalled properly I think.
That would be a neat enhancement in the future,
Many thanks,
Tuan
from nanocaller.
Does gvcf ever work practically though ? My efforts several years ago failed miserably with many undocumented bugs, others here have had the same experience completely independently. That's why I prefer multisample snp calling with a tool such as freebayes for short reads.
from nanocaller.
Related Issues (20)
- High coverage genotyping outputs only G HOT 10
- Using NanoCaller with BED files and Indel Calling Gives Empty VCF files HOT 3
- bcf tools error and error in whatshap HOT 4
- docker build fails due to missing NanoCaller_WGS file HOT 2
- Models compatible with Guppy6.x.x HOT 1
- Failed installation HOT 2
- bam file issue!
- what do you want to fill in the β--chromβ option? I read the instructions and there is no document. HOT 22
- header error in variant_calls.snps.phrased.vcf.gz HOT 6
- Unnormal results ! HOT 8
- AD (allelic depth) field HOT 5
- TypeError HOT 2
- Supporting reads HOT 3
- conda install incompatibilities HOT 2
- Models for R10.4.1 dorado
- Module not found tqtm after install with conda HOT 1
- Error phasing large chromosomes (550mb chromosome) due to inability to store as tbi index HOT 3
- Applications HOT 12
- indels HOT 2
- keras import issue by conda install
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 nanocaller.