VarSeq Custom Database Curation Capabilities

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About this webinar

April 13, 2022

Presented By: Darby Kammeraad, Director of Field Application Services

As our users have come to know, VarSeq serves as a hub for variant annotation and the full interpretation/classification of germline (ACMG) and somatic (AMP) variants. Whether direct annotation or backend variant evidence is being presented to the user via VSClinical for the interpretation process, users greatly benefit from the hosted variant databases being available directly from VarSeq. Our team has automated much of the curation process and hosts the ongoing updates to these tracks so that users no longer suffer manual review of each database via the web or manual curation efforts. Useful databases include ClinVar and ClinGen for classification submissions, gnomAD exomes/genomes for filtering out common variants in the population, RefSeq for gene impact and sequence ontology assessment, and OMIM for phenotypic information. Obviously, there is a large collection of databases out there, and not all of them make it into our automated queue. However, GHI supports the utilization of custom databases in our software. This webcast will expose features of custom database curation/utilization in VarSeq to optimize your NGS workflows even further. During the presentation, we will discuss many different approaches with custom annotations, including:

  • Interval Tracks: Bed files defining target regions for coverage calculations and CNV detection.
  • Assessment catalogs: record keeping of variant classification/interpretations in VSClinical.
  • Frequency catalogs: approaches to capture all variant allele frequencies at a project level and cohort level with VSWarehouse.

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