A common question that comes through support is if there are options in SVS for doing gender inference or checks. There is indeed functionality in SVS for this QC check! This function is under the Genotype Menu for Sample Statistics; there are a lot of great statistics available to check the quality of your data in SVS, but I’ll walk… Read more »
The support team at Golden Helix is always on-hand to help with your SVS and VarSeq needs. We get some questions more often than others, and this blog will answer some of the most common questions we’ve been seeing lately regarding VarSeq. A common question we receive is if data can be filtered from a locally kept set of variants… Read more »
Our VarSeq as a Clinical Platform webcast last week highlighted some recent updates in VarSeq that support gene panel screenings and rare variant diagnostics. The webcast generated some good questions, and I wanted to share them with you. If the questions below spark new questions or need clarification, feel free to get in touch with us at email@example.com. Question: Should… Read more »
Last month, Dr. Bryce Christensen presented Population-Based DNA Variant Analysis via webcast. The webcast reviewed the fundamentals of population-based variant analysis and demonstrated some of the tools available in SVS for analysis of both common and rare variants such as the SKAT-O method, as well as other functions for annotation, visualization, quality control and statistical analysis of DNA sequence variants. Here… Read more »
Our Genomic Prediction webcast in December discussed using Bayes-C pi and Genomic Best Linear Unbiased Predictors (GBLUP) to predict phenotypic traits from genotypes in order to identify the plants or animals with the best breeding potential for desirable traits. The webcast generated a lot of good questions as our webcasts generally do. I decided to begin to share these Q&A… Read more »
One frequent question I hear from SVS customers is whether whole exome sequence data can be used for principal components analysis (PCA) and other applications in population genetics. The answer is, “yes, but you need to be cautious.” What does cautious mean? Let’s take a look at the 1000 Genomes project for some examples.
“Who has ever had a bad experience with a VCF file?” I like to ask that question to the audience when I present data analysis workshops for Golden Helix. The question invariably draws laughter as many people raise their hands in the affirmative. It seems that just about everybody who has ever worked VCF files has encountered some sort of… Read more »
I recently gave a webcast on GWAS in a model organism: Arabidopsis thaliana; a question was brought up about the differences between EMMA and EMMAX and why the results with each would differ.