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.
A benefit of this service is that it provides access to this automated pipeline at a low cost ($1 for the first 10 Gigabases +$0.10/Gb after that) and is compliant with a multiple regulatory standards (ISOs 27001, 27018, and 9001 and HIPAA). …
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.
LumiraDx Antigen-Based Rapid Test
Let’s take LumiraDx’s SARS-CoV-2 Antigen test as an example. (This is a common antigen-based rapid test being offered at CVS Minute Clinics near me. It offers results in about 15 minutes using a nasal swab.) They report a sensitivity of 97.6% and a false positive rate of 3.4%, thus the Bayes Factor (aka Likelihood Ratio) is about 28.7. …
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