Assignment Date: Friday, Oct. 13, 2023
Due Date: Friday, Oct. 27, 2023
There are a bunch of command line tools you’ll need for both the live-coding and assignment. You’ll be creating a conda environment for this week that contains well-behaving versions of all of these tools. Create and activate a new variants conda environment for this week using the code below:
mamba create -n variants
mamba activate variants
conda config --env --set subdir osx-64
mamba install python=3.7 snpeff=5 freebayes bwa vcflib samtools
As always, before you do anything else, create a week5 directory in your qbb2023-answers directory for this assignment, and create a README.md file in that week5 directory. This is where you will be putting and uploading all of your code/plots/etc. for this assignment.
We would recommend creating a livecoding directory within your week5 directory, and putting your live-coding scripts and data there. You can add the livecoding directory to your .gitignore so that git won’t track these files.
Wherever you choose to do your live-coding, you can download the following file: https://www.dropbox.com/scl/fi/ye4h2eemcvsomsaccag4h/live_coding_data.tar.gz?rlkey=lgwmjno4ojojxbdwzj4fjamai&dl=0
This file contains the data you’ll need for the live-coding exercises. Once downloaded, unzip it with the following command:
tar -xvzf live_coding_data.tar.gz
Complete the homework assignment in your week5 submission directory in your qbb2023-answers.