Intro to HPC and Bioinformatics Precept

GitHub Assignment Link

This assignment will be completed excusively in Python This assignment will be due TWO weeks from the date of assignment

Overview

This precept will introduce you to the Adroit HPC cluster and basic bioinformatics tools. You will learn how to access the Adroit cluster, clone a repository, and run basic bioinformatics analyses. You will also learn how to use the vcftools tool to examine a Variant Call Format (VCF) file.

Make sure you document the commands you use to complete the exercises. Submitting a text file with these commands is sufficient.

Exercise 1: Accessing and Cloning a Repository on Adroit

Follow the guide for accessing the Adroit cluster.

• Objective: Learn to access the Adroit HPC cluster and clone a repository.
• Tasks:
  1. Use SSH to connect to the Adroit cluster. If you encounter a "Corrupted MAC" error, amend your SSH command: ssh -m hmac-sha2-512 <YourNetID>@adroit.princeton.edu
  2. Authenticate with GitHub! This may end up being a bit tricky. You may need to generate an SSH key and add it to your GitHub account. See this guide for more information.
  3. Navigate to your working folder: /scratch/network/[your YourNetID]
  4. Clone the desired repository: git clone [your assignment repository URL].

Exercise 2: Inspecting the VCF File

• Objective: Gain experience in handling Variant Call Format (VCF) files.
• Tasks:
  1. View the available modules on the Adroit cluster online.
  2. Load the anaconda3 module: module load anaconda3/2024.2
  3. Create a new conda environment: conda create -n [environment name].
  4. Activate the new environment: conda activate [environment name].
  5. Install vcftools in the new environment: conda install -c bioconda vcftools.
  6. Use vcftools to examine the contents of the VCF file.
• Output: The header of the VCF file. Please include the commands you used to generate this output.

Exercise 3: Measuring Individual Missingness and Simple Filtering

• Objective: Learn to use vcftools to measure missingness and filter on minor allele frequency.
• Tasks:
  1. Use vcftools to measure the missingness of each individual.
  2. Use vcftools to filter to sites with a minor allele frequency of at least 0.1.
  3. Repeat the missingness calculation on the new VCF file.

• Output: The missingness of each individual before and after filtering. Please include the commands you used to generate these values.

• Optional: Plot the missingness of each individual before and after filtering.