Hello Everyone,
q1) I have a set of VCF files and I would like to play around with it. I see in tutorials here and here that they do variant file analysis where they get the numbers. Does VCF file analysis using tools like Hail, bcftools mostly deal with summarising the information that is available in a huge VCF file? Or is the first part of VCF file analysis lifecycle?
q2) May I know-how does a VCF file analysis life-cycle look like and what are the different stages involved in it?
q3) What is the use of annotation? I did refer here but for a beginner any simple layman explanation can help. May I kindly check with you on why do we have annotate and what is the benefit of annotating VCF samples?
q4) Is there any end-end tutorial resource that you can share with me? Like how a real-world exhaustive VCF file analysis project would be like?
What exactly is your interest and aim with VCF files? Are you planning to use public VCF data (like 1000G) or do you have your own. Unless you describe your actual project in some reasonable detail all VCF questions you have posted so far are of general interest and answers you get may not be applicable to what you want to finally achieve.
Actually I don't have any specific project that I am working on. However, I am trying to learn and equip myself with this skill of VCF file analysis. I am assuming this may be part of genomic data analysis/science... So any tutorial which helps me/guides me with each stage VCF file analysis lifecycle would help. But yes, I have my own data. So, I am trying to make use of it. Instead of public datasets. Since I have the data, I can learn how to derive insights from this and then collaborate with other researchers in doing something meaningful. This is the plan. So, am basically trying to learn how to analyze the data that I have in VCF files