Please make sure each assignment is in its own folder, so we know what your final submission is.
Bash script that performs read alignment and variant calling/filtering/annotation
0/3
Exercise
Points Possible
Grade
Read alignment
1
0
Variant calling
1
0
Filtering and annotation
1
0
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
2/2
Total: 6.75/10
Nice work! For full credit:
Upload the Bash script you used for exercises 1 and 2.
Step 3.4: It looks like you're plotting Annotation_Impact information (line 80 in your VCF header), which does not give information on the types of predicted effects. Work with the information corresponding to Annotation instead.
Please make sure each assignment is in its own folder, so we know what your final submission is.
Bash script that performs read alignment and variant calling/filtering/annotation
0/3
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
3.75/4
Nicely formatted and labeled multi-panel plot showing summaries of exploratory analysis
2/2
Total: 6.75/10
Nice work! For full credit:
Annotation_Impact
information (line 80 in your VCF header), which does not give information on the types of predicted effects. Work with the information corresponding toAnnotation
instead.