---
title: "week 05 question set"
format: html
editor: visual
---

```         
a.**what are SAM/BAM files? What is the difference between to the two?**
SAM files are for sequence alignments, BAM files are for binary alignment data; Both of which are used for the storing of sequencing reads.

b.**samtools is a popular program for working with alignment data. What are three common tasks that this software is used for?**
The top three commond tasks are: samtools view, samtools sort, and samtools index. 

c.**why might you want to visualize alignment data and what are two program that can be used for this?**
If I am thinking about this properly then being able to visualize alignment data would be helpful for not only visually viewing quality control. It would also helps visualize any patterns. Sure you could run some function like grep, but SEEING is better. I believe NCBI works, which is what I know, but according to the reading you can also potentially use IGV (Integrated Genomic Viewer). I have never visually viewed sequencing data, so I am a little unfamiliar with specific programs.

d.**describe what VCF file is?**
A Variant Call Format (VCF) which is a plain-text tab-deliminated document you get after samtools arguments. Supposedly it generates the genotype liklihood for all genome sites in a given data file.
```