Computational biology and genomics
In this post, I describe a simple workflow for identifying Omicron variants from some sequencing data shared by the Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP) and the Centre for Epidemic Response and Innovation (CERI). To follow the workflow, you need to have Docker installed and an Internet connection. To get started, run a container…
Updated 2018 June 7th Just recently, the genome Aggregation Database (gnomAD) VCF files were available for download: The long-awaited gnomAD VCF is here – sites + frequencies for 123,136 exomes and 15,496 genomes: https://t.co/8puaTvJ45w pic.twitter.com/sxKOEVFDml — Daniel MacArthur (@dgmacarthur) February 27, 2017
In the age of 50,000+ and 60,000+ whole exome catalogues, it’s hard to find processed data for a single exome. At least I had trouble trying to find a single VCF file for a single exome from one individual. After searching for a while, I gave up and decided to generate one myself. This post…
I created a basic Shiny app that uses the myvariant package to fetch variant information from MyVariant.info. The variants need to be represented in the format recommended by the Human Genome Variation Society. Once you have your variant of interest in the correct format, just hit “Get variant info!” and the annotations will appear on…
A continuation of the post on the genomic location of pathogenic ClinVar variants. For this post I will use vcfanno to annotate the ClinVar variants with the ExAC VCF file. To get started, download the ExAC VCF file.
How many pathogenic ClinVar variants are in intergenic regions? I’ll define genomic regions as per this old post. To get started, download the latest ClinVar variants:
It has been almost two months since my last post; I have been occupied with preparing a fellowship application (which has been sent off!) and now I’m occupied with preparing and writing papers. Sadly, I’ve pushed blogging right down the priority list, even though it’s one of the things I enjoy doing the most. This…
After getting started and getting acquainted with DNA sequencing data, it’s finally time to explore DNA variation. A tool that makes this easy is GEMINI and this post briefly demonstrates some of its functionality. I have only used GEMINI sparingly and what I know about the tool is gathered mostly from their documentation and tutorials….