# Week 06 Questions

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

SAM/BAM files store read alignment data in an efficient way. SAM files are plain text and can be read by humans whereas BAM files store data in a binary form that allows the files to be smaller.

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

1. convert between SAM and BAM
2. extract alignments
3. sort alignments by chromosomal coordinates

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

You might want to visualize alignment data to better explore the data and see where insertions/deletions/mismatches, etc. occur. Visualzing allows you to navigate through the data in a way that is easier to understand and digeset. The tview command in samtools and the Integrated Genomics Viewer IGF can both be used to visualize alignment data.

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

VCF stands for Variant Call Format. It is a plain text tab-delimited file that holds the output of variant calls.