Opal 4.28 Release Notes

Charlene Son-Rigby -

 

4 April 2017

 

The Opal 4.28 release updates the Opal application with updated branding and associated application links, as well as data source updates.

 

Company Rebranding and Application Link Updates

Data Source & Algorithm Versions

 


Company Rebranding and Application Link Updates

On March 21, we rebranded our company. Omicia is now Fabric Genomics. In the Opal 4.28 release, we are updating the Opal application and domains to reflect our new name:

 

  • Help documentation will be moved to https://help.fabricgenomics.com. The Help link in the Opal application will automatically navigate to this site.
  • Support emails now come from support@fabricgenomics.com

  

Our company’s rebranding reflects the expansion of our vision and offering to an end-to-end computational genomics platform going from raw sequence data to clinical report. You can read more about our new name on our blog.

    


Data Source & Algorithm Versions

Opal Pipeline 6.0.11 - Released April 4, 2017

  • 1000 Genomes phase 3 version 5 (downloaded May 2, 2013)
  • CADD v1.0
  • ClinGen Dosage Sensitivity Project, ISCA Evidence (downloaded October 16, 2016)
  • ClinVar (downloaded March 27, 2017 - weekly release)
  • COSMIC v80
  • DGV Database of Genomic Variants (download May 15, 2016)
  • dbVar September 28, 2016 Release
  • dbNSFP version 2.9
  • dbSNP release 149
  • ENSEMBL version 83
  • ExAC 0.3 release
  • Exome Variant Server 6500 v0.0.30
  • Gene Ontology OBO  March 28, 2017
  • GeneSplicer  February 19, 2003
  • GERP++ 2010 release
  • Genome Reference Consortium Human Genome Build v37
  • GWAS catalogue (downloaded May 21, 2014)
  • HGNC and Entrez gene synonyms (downloaded March 16, 2017)
  • Human Phenotype Ontology1 build #124
  • Human Phenotype Ontology OBO March 9, 2017
  • MaxEntScan  September 25, 2003
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM (downloaded March 27, 2017)
  • PhastCons - phastCons46way (October 8, 2012)
  • PhenCode / LSDB (download April 30, 2014)
  • PhyloP - phyloP46way (December 1, 2009)
  • PolyPhen-2 v2.2.2 (dbNSFP v2.9)
  • RefSeq release 79 (November 7, 2016)
  • SIFT (dbNSFP v2.9)
  • SiPhy v0.5
  • UMLS version 2015AB (November 12, 2015)
  • VAAST Variant Prioritizer v1.1

 

1Sebastian Köhler, Sandra C Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucl. Acids Res. (1 January 2014) 42 (D1): D966-D974 doi:10.1093/nar/gkt1026

 

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