The Microsoft Genomics service in Azure is a cloud-based implementation of the Burrows-Wheeler Aligner (BWA) and the Genome Analysis Toolkit (GATK) for alignment and variant calling. This service came was released a few years ago and currently provides a Python 2.7 CLI to submit workflows. This software takes in either a pair of .FASTQs or a .BAM file and outputs a .VCF based on a human reference genome of your choice.
If you watch or read the news, there are a flurry of reports of SARS-CoV-2 variants popping up in the US and around the world. Some reports generalize and might say something like “The South African variant was found in South Carolina” or “The E484 variant was seen in Massachusetts”. This can be confusing as the media’s coverage of this is a little vague and maybe a bit misleading.
In this post, I want to bring everyone up to speed about what qualifies as a variant and how it relates to public health in this COVID-19 pandemic.
In the realm…
Over the past couple weeks, friends and family have asked me questions about the “accuracy” of different COVID-19 tests. This video by #3Blue1Brown explains why accuracy isn’t really what you’re wanting to know. A better question would be: “Given a positive test result, what’s the probability I actually have COVID-19?” or, in his terms, you want to update your assumed likelihood of having COVID-19 once you get a test result. Test accuracy only determines how your chances of having a disease are updated but does not by itself determine your chances.
Let’s take LumiraDx’s SARS-CoV-2 Antigen test as an example…
Computational Biomathematician and Cloud AI Guy. I research machine learning and genomics and I sometimes write things here.