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.
Bash script that performs read alignment and variant calling/filtering/annotation
2.75/3
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
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 forfreebayes
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.vcffilter
.