a)  **What are SAM/BAM files? What is the difference between to the two?**

SAM is Sequence Alignment/Map and BAM is Binary Alignment/Map

| SAM | Both | BAM |
|-----|------|-----|
| plain text | store read alignments | binary
| larger | space-efficient and complex | compressed/ smaller
| slower |   | faster |
| human readable | | not human readable

b)  **`samtools`is a popular program for working with alignment data. What are three common tasks that this software is used for?**

You can convert between the different formats (SAM/BAM/CRAM), manipulate alignments, sort, merge, index.
You could identify SNPS, detect other variants, or quantify gene expression.

c)  **Why might you want to visualize alignment data and what are two program that can be used for this?**

You can use samtools tview and Integrated Genomics Viewer to visualize alignment data.
It's good to view your data so you can see the alignments, variants, or inspect insertions and deletions.

d)  **Describe what VCF file is?**

VCF is a Variant Cell Format file. Its a plain-text tab-delimited format with three parts. It has a metadata header, a header line with eight mandatory fields and sample names, and data lines containing information for a variant at a particular position and all individuals’ genotypes.
Also has binary counter part BCF.