A New and Unexpectedly Powerful VarSeq Feature


With the release of VSReports, we added the ability to “select” rows of your filtered output (often variants, but potentially things like coverage regions or genes) with a new feature dubbed “Record Sets”, but more often described as “colored checkboxes” for your tables. Although necessary for the important task of marking primary, secondary or other sets of variants for a… Read more »

OMIM Coming to VarSeq

      Gabe Rudy    September 1, 2015    7 Comments on OMIM Coming to VarSeq
Update to SVS

When it comes to down to it, the genomic variants we collect in a research and clinical setting are impossible to interpret without that important link of how genes are related to phenotypes. Indisputably, the Johns Hopkins project to catalog all evidence related to inheritable Mendelian diseases is our best repository of this evidence. Online Mendelian Inheritance in Man (OMIM)… Read more »

Between Two Bases: Coordinate Representations for Describing Variants


Have you ever scratched your head when looking up a variant and it seems like the number you have for its position is one off from what it looks like in the file or database? You may be running into the dreaded world of 1-based versus 0-based coordinate representation! If it’s any consolation, I can promise that all the bioinformaticians… Read more »

Analyze Your 23andMe Genotype Files with Golden Helix


I was definitely an early adopter when it comes to personal genomics. In a recent email to their customer base announcing their one millionth customer, they revealed that I was customer #44,299. And I have been consistently impressed with the product 23andMe provides through their web interface to make your hundreds of thousands of genotyped SNPs accessible and useful. It… Read more »

The Clinical Genome Conference 2015 Highlights

This last week I had the pleasure of attending the fourth annual Clinical Genome Conference (TCGC) in Japantown, San Francisco and kicking off the conference by teaching a short course on Personal Genomics Variant Analysis and Interpretation. Some highlights of the conference from my perspective: Talking about clinical genomics is no longer a wonder-fest of individual case studies, but a… Read more »

VarSeq is a better ANNOVAR, snpEff and VEP

Yes, I said it. “Them be fighting words” you may say. Well, it’s worth putting a stake in the ground when you have worked hard to have a claim worth staking. We have explored the landscape, surveyed the ravines and dangerous cliffs, laboriously removed the boulders and even dynamited a few tree stumps. Stake planted. Ok, so now I’m going… Read more »

Accurate Annotations: Updates to the NHLBI Exome Sequencing Project Variant Catalog


Since its early release in early 2012, the population frequencies from the GO Exome Sequencing Project (ESP) – from the National Heart, Lung and Blood Institute (NHLBI) have been a staple of the genomic community. With the recent release of ExAC exome variant frequencies, the ESP has been surpassed as the largest cohort of publicly available variant frequencies (by nearly… Read more »

Unique Labs, Common Tool: Making VarSeq Ready for Clinical Workflows

As VarSeq has been evaluated and chosen by more and more clinical labs, I have come to respect how unique each lab’s analytical use cases are. Different labs may specialize in cancer therapy management, specific hereditary disorders, focused gene panels or whole exomes. Some may expect to spend just minutes validating the analytics and the presence or absence of well-characterized… Read more »

Supercentenarian Variant Annotation: Complex to Primitive

In a previous blog post, I demonstrated using VarSeq to directly analyze the whole genomes of 17 supercentenarians. Since then, I have been working with the variant set from these long-lived genomes to prepare a public data track useful for annotation and filtering. Well, we just published the track last week, and I’m excited to share some of the details… Read more »

What TriCon 2015 Foreshadows for Clinical Genomics

I spent a very eventful week at the Molecular TriCon in downtown San Francisco, and have been pondering the very clear trends that emerged by attending the clinical and NGS focused talks. Cancer gene panels make sense economically and as “massively parallel” tests to inform therapy, but they are bound to get more complex. Liquid biopsies of circulating tumor DNA… Read more »