Author Archives: Darby Kammeraad

Darby Kammeraad

About Darby Kammeraad

Darby Kammeraad is the Field Application Scientist Manager at Golden Helix, joining the team in April of 2017. Darby graduated in 2016 with a master’s degree in Plant Sciences from Montana State University, where he also received his bachelor’s degree in Plant Biotechnology. Darby works on customer support and training. When not in the office, Darby is learning how to play guitar, hunting, fishing, snowboarding, traveling or working on a new recipe in the kitchen.

Custom Filtering using ClinVar Annotations

ClinVar

ClinVar is one of our most used annotations sources for a variety of workflows. It is also the public annotation source that is updated most frequently of all the sources currently supported in VarSeq. ClinVar provides new versions of their database once a month in several formats (XML, VCF, TXT). We use custom Python scripts to convert the provided VCF… Read more »

Whole Exome Sequencing workflows in VarSeq

Whole Exome Sequencing Workflows

Whole exome sequencing workflows using SNP & Variation Suite (SVS) was presented in a recent webcast, by Dr. Robert Hamilton from the Hospital for Sick Kids. In particular, he performed some filtering on his data to look for only heterozygous variants in his sample of interest, removed variants with allele frequency less than 0.005% based off of the ExAC Variant Frequency… Read more »

Customizing Workflows for Family Structure

family structure

During the webcast yesterday, I demonstrated a few ways of customizing de Novo Candidate and Compound Heterozygous Candidate workflows to consider family structure that was slightly different from the default trio workflow. The families included additional affected and unaffected siblings added to a trio as well as looking at what could be done if there were only two affected siblings… Read more »

Solving the Eigenvalue Decomposition Problem for Large N

Eigenvalue Decomposition

Solving the Eigenvalue Decomposition Problem for Large Sample Sizes Since our introduction of the mixed model methods in SVS, along with GBLUP, we have been very pleased to see it used by a number of customers working with human and agri-genomic data. As these customers have grown their genomics programs, the number of samples they have for a given analysis… Read more »

N-of-One Integration comes to VSReports

Submit directly to N-of-One from VarSeq If you or your lab uses N-of-One solutions for clinical annotations, here’s some good news: You can now submit directly to N-of-One from VarSeq! N-of-One’s set of preferred transcripts may differ from those outputted by our algorithms in VarSeq, so our solution was built with that in mind. Our slick, easy to use, and… Read more »