Comments (1)
Hi,
Sorry for the late response. SCAN-SNV is currently only a somatic caller and does not call germline SNVs. If you'd simply like to get the list of germline sites, you can parse the GATK output yourself. The file is here: <scansnv_output>/gatk/hc_raw.mmq60.vcf.
I would start by extracting the column corresponding to your bulk input from that file and finishing the GATK best practices workflow by running VQSR. After the final germline calls are generated by VQSR, you could then return to the hc_raw.mmq60.vcf file to extract the germline sites for each single cell.
Hope this helps.
from scan-snv.
Related Issues (7)
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 scan-snv.