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title: "Week 06 Questions"

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a)  **What are SAM/BAM files? What is the difference between to the two?**
SAM is a Sequence Alignment/Map file format and BAM Binary Alignment/Map file format. Their difference is SAM is a Sequence alignment and BAM is a binary alignment. 

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

Three common tasks this software is used for are for Sorting and Indexing, Quality control, and Variant calling. 

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 this data because visualizing the data would you let you understand the quality of your data and may let you find if there are errors. Two main programs would be IGV (Integrative Genomics Viewer) and Tablet.
d)  **Describe what VCF file is?**

VCF is a Variant Call Format (VCF) file is a standardized text file format used in bioinformatics to store variations, or differences, in the genome sequence of individuals or populations relative to a reference genome.