baezortega / somatypus Goto Github PK
View Code? Open in Web Editor NEWA Platypus-based variant calling pipeline for cancer data
A Platypus-based variant calling pipeline for cancer data
Hi,
I encountered an issue using Somatypus in the genotyping stage.
(8) PREPARING DATA FOR VARIANT GENOTYPING
Traceback (most recent call last):
File "/hgsccl/next-gen/scratch/chander/software/somatypus/src/Somatypus_ExtractRegions.py", line 138, in
start = int(exonComp[1].split('-')[0])
IndexError: list index out of range
ERROR: Output file /hgsccl/next-gen/scratch/chander/somatypus_out/8-18_genotyped/was not correctly generated. Please check the logs folder for more information.
Any thoughts why this error occurs?
Best,
Varuna
Yo man, your tool here is nice - but I can no longer accept the discriminatory nature of your code against organisms with large chromosomes!
I mean really large chromosomes, larger than yours. Think about marsupials, for example. Plants, big genome plants. Or what would the Marbled lungfish say if you can't run somatypus on him? "Speciesism!"
CSI indexing on VCFs and BAM files is the future, I tell ya bro. Check out my brand new golden changes to your core bash script, here attached.
No questions. Peace out.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 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. 📊📈🎉
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 ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.