Hi all. We're Basepair, a platform that allows researchers without any programming skills to analyze next-generation sequencing data themselves. We host monthly bioinformatics webinars and are excited to share a lot of good content on variant calling during tomorrow's webinar.
The webinar is great for bench scientists/ those who don't have much bioinformatics experience. Register on our website. If you can't attend the live stream, you can still register and we'll send you a link to the recording after the webinar.
We'll be covering:
Tips on designing your experiment. We will walk you through some of the more important questions to consider when planning your experiment. Should you go with WGS, WES, or a panel? What depth of coverage should you choose? And if you’re sequencing tumors, what is the purpose of a normal control or a panel of normals?
What are the tool and parameter best practices? We will provide a quick comparison of some variant callers and guide you on which you should choose depending on your needs. Moreover, among the dozens of parameters these tools have, we will talk about those you may want to change and how they could impact your analyses.
How to tell if your data is poor quality, and what to do about it. We will guide you through some key metrics and plots, including read quality metrics, mapping metrics, and coverage. You will learn about approaches you can take to mitigate poor quality data.
Ways to validate your variant calling results. How can you check if your variant calls are real? We will highlight key variant metrics to examine, show you how to use the genome browser, and discuss why you might want to consider Sanger sequencing or targeted deep sequencing for further validation.
We want to be totally transparent that we're a for-profit company, and during the webinar, we will be showing you variant calling pipelines from our GUI and not from the command line. That said, this webinar is going to have a lot of useful content for the less computationally experienced researchers and the tools we mention are available as open-source software.
