VCF and SAM Parsing with grep, sort and awk, plus API Retrieval in R

Command-line and R work on real genomic files, written up in R Markdown.

The exercises are deliberately unglamorous and, for that reason, the ones that get used daily:

• Reading large files without opening them. Pulling the header out of a large VCF with grep and tail. Sequence data routinely exceeds what an editor will load, so the shell is what lets you inspect and subset a file you cannot open.
• Counting what is actually there. A SAM file with 17,608 lines but only 8,804 unique read names, established with sort and uniq. The gap between those two numbers is the point.
• Repairing malformed data with awk.
• R fundamentals: vectors, loops and data cleaning.
• Working against a live API: retrieving UK COVID-19 case data from the coronavirus.data.gov.uk API and filtering it by date.