Related Issues (20)
- Spec out existing exome functionality
- Transfer all of the bam files including genentech ones
- Investigate variants that RUFUS didn't call from gold-standard dataset - specifically those that had contigs made but no variant calls HOT 1
- Investigate why there is a sensitivity issue for 120X 90-95% AF variants (FD-all samples from seqc2 consortia)
- Get rid of leftover pipes during RUFUS run
- Change 1000G filter to gnomAD one HOT 1
- Test container on slurm system for CHPC
- Add SG's inherited variants filter to main script to run post vcf generation HOT 1
- Make documentation regarding build more clear - e.g. the 1000G file needs a build in it or change command line option to just use a build instead of specifying ref/1000G file
- Gather what base numbers are for rufus vcf filters + add ability to let user specify filtering cutoffs (for SG VQS project)
- Determine source of non-determinism in rufus output HOT 1
- Add actual read count output and fraction per variant in vcf instead of just kmer counts
- Include indels greater than 50bp in SVTYPE label HOT 1
- Fix no genotype lines in VCF that bricks post-processing HOT 2
- Remove extraneous files from RUFUS output (fastas, hash tables) & appropriately rename retained files (like contig bam)
- Fix stdout/stderr to actually provide concise and helpful output
- Add 1mb mode to arguments
- Add inherited removal at end of rufus run for either combined file or single run
- Make small test set for 1mb mode and single mode
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 rufus.