Computational biology and genomics
From the original paper describing the Gene Set Enrichment Analysis: The goal of GSEA is to determine whether members of a gene set S tend to occur toward the top (or bottom) of the list L, in which case the gene set is correlated with the phenotypic class distinction.
The Variant Effect Predictor (VEP) tool can be used for annotating variants with respect to custom annotation sources. This is useful if gene models of interest are not represented in the Ensembl or RefSeq databases. To get started, first install VEP since it takes some time.
I have started to work on Arabidopsis thaliana, as I mentioned in my last post. As noted in the Encyclopedia of life: Arabidopsis thaliana is the most widely used model organism in plant biology. Its small genome size, fully sequenced in the year 2000, chromosome number, fast growth cycle (from seed germination to set in…
What’s the difference between deleteriousness and pathogenicity? Box 1 from the article “Guidelines for investigating causality of sequence variants in human disease” has the following definitions:
The American College of Medical Genetics and Genomics (ACMG) have recommended that genetic variants that may be pathogenic or likely pathogenic in certain genes should be reported back to the patient. The latest list of genes can be found here. How do I assess whether a variant is pathogenic or likely pathogenic? Use this tool,…
I’m a fan of GEMINI and have been using it for for a year and a half for various exome projects. I have written two scripts that can generate variant summaries from a GEMINI database. I prefer bar plots over the pie charts created by VEP. A summary pie chart created by VEP.
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
Update 2017 May 10th: I realised that this approach doesn’t work for all genes, unfortunately. For example, the gene TTN (which is an HGNC approved gene symbol) is associated with 600334, 603689, 604145, 608807, 611705, and 613765 but biomaRt returns an NA. Please refer to an updated post. I was interested in the number of…
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…
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.