README.md

Week 6: Variant calling

Now that we have reads aligned to our genome we can look for areas where they differ. We will use bcftools to call small genomic variants and manipulate the resulting files. Now that we have a "complete" analysis, we will talk about basic shell scripting and creating pipelines.

Learning Objectives

• List comonly used variant callers and their advantages & limitation.
• Employ bcftools to call varaints in snowflake yeast.
• Use bcftools to filter variants by quality.
• Read basic information from variant call formatted files.
• Write a variant calling pipeline.

Assignment and Project

This week we'll work primarily on our projects this week.

• In your project directory, create a file called methods.md and create a reference and link to it in your main README.md file.
• Use this file to enumerate the analysis steps of your pipeline.
• Use section headers # , ##, and ### to organize your document.
• Use ticks to put example commands.
• Describe the inputs and outputs of commands.
• Denote which files can be used across multiple samples.
• Note which files are "worth saving" and which are just temporary steps in the pipeline that should be cleaned up.

After this, try making a script that accomplishes these tasks.