Greetings! If you're reading this you've been welcomed into the wheeler lab for the semester. Congradulations! This collection of documents will serve as a guide for some of the various tools you'll be using this semester. By no means is it comprehensive, but the hope is that it will serve as a directory to point you towards more useful resources, including tutorials, cheat sheets, papers, twitter threads, SOPs, and manual pages. Most of the lab is catered towards independent problem solvers. Feel free to shoot any of the senior members a message for help, but you learn the most by just trying. Good luck and get to work!
Everything on this list are things you are likely to use. It has beed divided according to programming language/interface and ordered by how useful I find it, though many of these rankings are arbitrary as I use most of these tools every day.
- awk x (Also see my awk cheat sheet !)
- plink x
- qsub
- aliases check out my mini guide to aliases
- PrediXan/PredictDB
- sed
- git
- vcftools/bcftools
- liftOver
- dplyr x
- data.table
- argparse
- rstudio
- dev tools
- manhattan/qqplots
- pandas
- numpy
- argparse
- Sanger imputation guide x
- Michigan imputation guide
GWAS QC pipeline x
- Check out this gist that walks through the steps if you get stuck x
- Also be sure to check out the project wiki in github