Comments (1)
juliawiggeshoff
commented on September 2, 2024
1
@maximus3219 I don't know if you are still interested but I had the same problem last week. I wrote a Python script to calculate VAF for indels and snvs from the somatic VCF files. I couldn't get it done with bcftools either, but here is the script. It calculates the VAF for each variant and includes this information for the normal and tumour samples in the final output vcf. Usage instructions are on the README.md
from strelka.
Related Issues (20)
- CONFIGURATION ERROR: Reference genome mismatch:
- Which command to use for somatic calling and RNA sequencing?
- Long error using the code below
- How to detect somatic mutations with allele frequencies nearly 0.01? HOT 1
- Only the first Genome Segment called when putting entire chromosome in .bed file
- inconsistent reproducibility of variants
- Number of AD, ADF and ADR should be "R"
- Failing to index VCF file
- Incorrect handling of non-N nucleotides with quality zero after Q-score binning
- All variants being labeled as "LowEVS" HOT 1
- Meaning of taskExitCode -9 HOT 1
- Include AD (allelic depths) in format from somatic variants HOT 1
- Strelka filtering out important variant
- GQ and PL fields
- DEVELOPER_MODE is true in src release tarballs
- how to install strelka on linux? HOT 3
- call mtDNA variants from scRNA or WGS
- Python3 HOT 1
- Error calling bam files derived from standard ONT
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 strelka.