Step 7 ‐ Analysis - aduckwo4-boop/EPP622-2026-SNPCalling GitHub Wiki

Assignment Analysis - Questions to answer

Minimum one paragraph each.

How did samples differ from each other in read count versus in read quality? Why does each matter for SNP calling?

What are the relative merits and drawbacks of filtering? Interpret the above chart in terms of the original quality issues, and how those yielded different outcomes. When is filtering a good idea vs when it is it a bad idea? Think specifically about false positives vs false negatives.

Pick two false negatives and two false positives, from any sample. For each, tell me the sample, tell me the chromosome and coordinate location, put in a screenshot of IGV or JBrowse, and explain the specific cause of the FN or FP call.

AI Analysis - Pipeline Audit

This is an evaluation of the pipeline you generated at the beginning of the learning module. Provide full sentences and thoughtful rationale.

Model used:

Date generated:

Exact prompt:

Minimum one paragraph each.

Three things it got right.

Three things you don't understand and would want to learn more about before using. Or do you understand all of it? If so be ready to answer questions about it.

How specifically would you assess the results of this pipeline for accuracy?

What did the labs teach you that turned out to matter for evaluating the AI-generated code?

What is the value of learning about a computational genomics task before using AI for it — or is there none?