Problem Set 4

This assignment is worth 15% of your final grade. It is graded out of 100 points.

Objectives

• Gain experience using standard short read alignment, genotyping, and visualization techniques.
• Learn how to detect artifacts in alignment or variant calling that can arise from next generation sequencing analysis.
• Learn how to use methods for filtering and prioritizing variants in medical NGS studies.
• Explore new long read sequencing technologies.

Data for this problem set is provided in /datasets/cs284-sp21-A00-public/ps4.

This problem set consist of 4 parts, each in a separate notebook so that you can work on each problem + validate the notebook separately:

• CSE284-PS4-PART1.ipynb: Sequence alignment and visualization (15 points)
• CSE284-PS4-PART2.ipynb: Writing a simple SNP caller (35 points)
• CSE284-PS4-PART3.ipynb: SNP calling with long reads (25 points)
• CSE284-PS4-PART4.ipynb: Mutation hunting in Kabuki Syndrome (25 points)