Opal 5.0 Release Notes

Charlene Son-Rigby -

 

08 July 2017

The Opal 5.0 release upgrades the annotation pipeline to VEP Version 88.13. 

Data Source & Algorithm Versions

Opal Pipeline 6.1 - Released July 8, 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 June 5, 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  April 13, 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 #127
  • Human Phenotype Ontology OBO April 13, 2017
  • MaxEntScan  September 25, 2003
  • MutationTaster (dbNSFP v2.9)
  • NNSplice v0.9
  • Omicia Score v2.0
  • OMIM (downloaded May 31, 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 80/81
  • SIFT (dbNSFP v2.9)
  • SiPhy v0.5
  • UMLS version 2017AA (May 8, 2017) 
  • VAAST Variant Prioritizer v1.1
  • VEP2 version v88.13

 

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

2McLaren et. al. 2016 (doi:10.1186/s13059-016-0974-4)

 

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