itsvenu / signatures-manuscript Goto Github PK
View Code? Open in Web Editor NEWMutational Signatures extraction - Pediatric cancers
Mutational Signatures extraction - Pediatric cancers
Dear Venu,
I hope this message finds you well. I really appreciated your great manuscript about mutational signatures in pediatric cancer, since I am also working on MSs in pediatric leukemia.
I read that you used a DKFZ in-house pipeline for variant calling, but also combined results with Mutect2. I am using Mutect2 (tumor-normal mode) for variant calling and I have encountered many issues with tumor-in-normal contamination and found active regions being completely excluded from Mutect2 somatic calling (normal-control samples were contaminated in some cases).
Of course, this is very deleterious for the subsequent MSs detection, since many true somatic variants are not called by Mutect2 and missed in the signature matrixes generation.
Did you also faced this issue? Is your pipeline optimized in order to perform a better calling of somatic variants, using matched controls and maybe whitelisting some known hotspots?
Thanks in advance for your kind answer.
Alberto
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.