Comments (3)
Clair doesn't use the soft-clipped bases. Have you disabled showing the soft-clipped bases in IGV?
from clair.
Yes, I have disabled soft-clip view.
Here is the test files I used. You might check it in details.
The vcf is generated by following command. Coverage difference is on 17707 (443 vs 476)
python $clair callVarBam --haploid --chkpnt_fn $model --ref_fn $ref \
--bam_fn $bam --ctgName $contig_name --sampleName "test" --call_fn "test.vcf"
from clair.
Please set "-dcov 500" when running callVarBam.py
. It increases the limit of the number of reads starting at each genome position from the default 250 to 500.
from clair.
Related Issues (20)
- Specific use case HOT 1
- quality threshold advice HOT 1
- Clair and Clairvoyante having trouble with bam file from human transcript alignments HOT 1
- Automatically call SNPs for all contigs in fasta file? HOT 2
- model quantization experiments HOT 2
- Demo Error: Missing testingData HOT 2
- Any chance of a clair model trained on guppy >=3.6.0, and on guppy 4.4.2 with bonito? HOT 4
- ValueError: invalid literal for int() with base 10: 'CCA' HOT 1
- Quality cut off determination for CLR data HOT 1
- problem during training HOT 1
- sars-cov2 model HOT 1
- Models for guppy v5 basecalled Nanopore data HOT 1
- ONT R9.4.1 vs R10.3 HOT 1
- HETEROSNP is not defined in the header HOT 1
- Which Reference to use during Training? HOT 1
- downsampled BAM cannot download HOT 1
- Clair force calling using callVarBam calls more number of variants than included in a vcf file. HOT 3
- error using on HPC HOT 1
- cram file support ? HOT 1
- Running issue!!
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 clair.