---
title: "05.hw"
output: html_document
date: "2025-04-29"
---

What are SAM/BAM files? What is the difference between to the two?
SAM files are sequence alignment map and BAM files are binary alignment map, they are different formats for alignment data. BAm files are compressed, non-human readable and can be used for faster computational processing and can be indexed.

samtoolsis a popular program for working with alignment data. What are three common tasks that this software is used for?
convert between formats
sorting and indexing bam files
extracting reads by region
Why might you want to visualize alignment data and what are two program that can be used for this?
so you can QC your data, visuallly look at vairants, and inspect expression. 

Describe what VCF file is?
A VCF file has intermediate variant and genotype data for a region or entire genome. 
The file has a metadata header, a header line, and data lines.