Week 5 Feedback

[schidambaran]

Please submit your assignment for week 5.

Bash script that performs read alignment and variant calling/filtering/annotation

2.75/3

Exercise	Points Possible	Grade
Read alignment	1	1
Variant calling	1	0.75
Filtering and annotation	1	1

VCF file containing the first 100 lines of your filtered/annotated VCF from Step 2.4

1/1

Python script that runs exploratory analysis of VCF from Step 2.4

3.75/4

Exercise	Points Possible	Grade
Code to parse VCF file	2	1.75
Code to produce multi-panel plot	2	2

Nicely formatted and labeled multi-panel plot showing summaries of exploratory analysis

1.5/2

Total: 9/10

Great work! For full credit:

• Step 2.2: This data comes from haploid yeast strains, so -p should be 1 for freebayes.
• Step 3.4: There are several more predicted effects. Loop through the ANN field in your VCF to find them all.
• Exercise 3: Label all the x-axes on your plots.