29 September 2017
The Opal 5.2 release upgrades the annotation pipeline with updates for ClinVar, dbSNP, OMIM, and VEP; and also contains various feature enhancements.
Feature Enhancements
VAAST and Phevor:
- VAAST and Phevor annotations can now be exported via the API
- VAAST Manhattan plot now displays p-Value by default, with the option to display by VAAST Score
Structural variant (SV):
- Filtering by de novo mode of inheritance in trios
- Display of percent overlap of SVs with previously classified SVs
Clinical Report workflow:
- Clinical report data for variant triage and classification can be copied to a new report using the "Import Candidate Variants" option
Data Source & Algorithm Versions
Opal Pipeline 6.2.2 - September 29, 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 (2017-09 monthly XML release)
- COSMIC v82
- DGV Database of Genomic Variants (download May 15, 2016)
- dbVar September 28, 2016 Release
- dbNSFP version 2.9
- dbSNP release 150
- ENSEMBL version 83
- ExAC 0.3 release
- Exome Variant Server 6500 v0.0.30
- Gene Ontology OBO August 17, 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 August 9, 2017)
- Human Phenotype Ontology1 build #129
- Human Phenotype Ontology OBO June 30, 2017
- MaxEntScan September 25, 2003
- MutationTaster (dbNSFP v2.9)
- NNSplice v0.9
- Omicia Score v2.0
- OMIM (downloaded September 8, 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 v89
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-
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