Category Archives: Bioinformatic support

Sentieon’s Secondary Analysis Tools Explained

Sentieon's Tools

We find ourselves talking a lot about our partnership with Sentieon … and more specifically, extolling the powerful, comprehensive genomic data analysis solution we are now able to offer clients. Sentieon’s suite of secondary analysis tools made a significant improvement in runtime over BWA-MEM, GATK, Mutect, and MuTect2 while providing deterministic and identical results. Here are two fantastic white papers that… Read more »

Top 10 Posts for Understanding Clinical Annotation of Genomic Variants

Top 10

The VarSeq clinical platform is built on a strong foundation of data curation and annotation algorithms to ensure the variants identified have all the information required to make the correct clinical assessments.  It’s easy to make light of “variant annotation”, but the details run very deep into the roots of how we represent genomic data, how public data is aggregated, stored… 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 »

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 »

Using Assessment Catalogs in your VarSeq workflow

Variant Assessment Cataloug

Variant interpretation is an integral part of any workflow that results in some decisions being made about the validity and suspected functional impact of a variant in a given sample and their presenting phenotypes. The VarSeq Assessment Catalog functionality is designed to assist the VarSeq user in streamlining this process. To include this functionality in your workflow, you will first… Read more »