Week 5 Feedback

[schidambaran]

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	1
Filtering and annotation	1	0.75

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

3.5/4

Exercise	Points Possible	Grade
Code to parse VCF file	2	1.5
Code to produce multi-panel plot	2	2

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

1.5/2

Total: 8.75/10

Good work! For full credit: , please submit the rest of the assignment and:

* Step 2.2: This data comes from haploid yeast strains, so you should be using the -p flag for freebayes to specify the correct ploidy. Also, freebayes needs to be run for all the samples at once and not in a loop. The -L flag could help with this.

• Step 2.2: Quality scores are given in the Phred format, so you need to give a Phred score cutoff to vcffilter.
• Step 3.4: To get the list of predicted effects, such as "missense_variant" and "upstream_gene_variant", look at the information after ANN. The format of ANN can be found in line 80 of your VCF.
• Exercise 3: Please make sure all the text on your plots is readable, and that your graphs are scaled appropriately.

[schidambaran]

Your grade has been updated!