Author Archives: Gabe Rudy

About Gabe Rudy

Meet Gabe Rudy, GHI’s Vice President of Product and Engineering and team member since 2002. Gabe thrives in the dynamic and fast-changing field of bioinformatics and genetic analysis. Leading a killer team of Computer Scientists and Statisticians in building powerful products and providing world-class support, Gabe puts his passion into enabling Golden Helix’s customers to accelerate their research. When not reading or blogging, Gabe enjoys the outdoor Montana lifestyle. But most importantly, Gabe truly loves spending time with his sons, daughter, and wife. Follow Gabe on Twitter @gabeinformatics.

  

Springtime for SVS: Updates to PhoRank, Platform Support and Genotype Imputation

VarSeq Updated

Recently, we added a natively supported Genotype Phasing and Imputation capability in SNP & Variation Suite 8.7.0. Since then we have had fantastic feedback and adoption as folks take advantage of the BEAGLE 4.0 and 4.1 algorithms from within their existing SNP GWAS and agrigenomic workflows. One piece of feedback we heard from our time at PAG, ACMG and our… Read more »

Updating VarSeq’s Transcript Annotation along with NCBI RefSeq Genes Interim Release

transcription annotation

It may be possible to say that annotating a variant correctly and accurately against gene transcripts is the most important job of a variant annotation and interpretation tool. We take it very seriously at Golden Helix as we support VarSeq and its use by our customers in both research and clinical contexts. It has been a source of frustration that… Read more »

Paying Attention to the Quality Fields in ExAC: A Case Study

In the past couple of weeks, the topic of the Filter and Quality fields in the popular ExAC population catalog has come up a number of times. It turns out that unlike the 1000 Genomes project, which decided to very heavily filter their variant list to only contain variants they consider high quality, ExAC chose to include more dubious variants… Read more »

PhoRank in SVS: Gene Ranking for Your Research Genotypes

gene ranking

Since we released our Phenotype Gene Ranking algorithm in VarSeq, it has become a staple of the way people conduct their analysis. It allows for a combination of filtering with ranking to prioritize follow-up interpretations of analysis results. Our PhoRank algorithm will be available in our upcoming SVS release to also aid in the numerous research workflows performed on SNPs… Read more »

Massive Variant Boost to ClinVar & PubMed Citation Fields

ClinVar

It may have been easy to miss in the drum-beat of monthly annotation updates we do here at Golden Helix, but there are a couple of things that are very special about the January update to the ClinVar database: We added new fields including HGVS names of variants and citations in PubMed for variants ClinVar nearly doubled in size by… Read more »