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.

  

CNV Caller Updates and More with VarSeq 1.4.5

Genotype Imputation

We have been heads down doing the detailed and careful work to improve our CNV caller algorithm in the past three months since our we launched our Exome capable CNV caller and are very excited about the massive step forward we have made with the VarSeq 1.4.5 release. Additionally, we have added the all new Whole Genome large-event caller capable… Read more »

Annotating with gnomAD: Frequencies from 123,136 Exomes and 15,496 Genomes

annotating gnomAd

Annotating with gnomAD: Frequencies from 123,136 Exomes and 15,496 Genomes When the Broad Institute team lead by Dan MacArthur announced at ASHG 2016 that the successor to the popular ExAC project (frequencies of 61,486 exomes) was live at http://gnomad.broadinstitute.org/, I thought their servers would have a melt-down as everyone immediately jumped on and started looking up their favorite genes and… Read more »

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

SVS platform

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 »