#Homework Week 06

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

They are both ways to store aligned sequences without taking up so much space. SAM files are in plain text and BAM files are in binary, so SAM files are human-readable but BAM files take up less space.

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

This software can be used to convert between SAM and BAM files, merging BAM files, and indexing BAM files.

*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 inspect how different sequences are, how many gaps were created during alignment, or manually change the alignment. Two programs that you can use for this are tview in samtools and the Integrated Genomics Viewer (IGV).

*d. Describe what VCF file is?*

VCF is a variant call format file, which contains information on gene variants in each position of the alignment and the associated metadata.