If you work with human samples and have Internet access, ArrayStar’s Variant Annotation Database lets you retrieve annotation information from DNASTAR’s cloud database for each of the variants in a specified region. The Variant Annotation Database is like having an enriched VCF file for the entire human genome that takes up no space on your computer.
The Variant Annotation Database is human-specific and contains variant information using coordinates from GRCh37 (hg19) and GRCh38. Annotations include information about the frequency of the variant in the general population or in a specific population, as well as information concerning the variant’s impact on functionality. The annotation information comes from several sources:
1000 Genomes Project and the Exome Sequencing Project (ESP):
•Allele and genotype frequencies. (Note: these are only available for build 37 assemblies, not for build 38).
dbNSFP v 3.3:
•Functional impact predictions from Sorting Intolerant from Tolerant (SIFT), MutationTaster, and the Likelihood Ratio Test (LRT).
•Evolutionary conservation scores from SiPhy, PhyloP, PhastCons and GERP++.
•Pathogenicity and clinical significance impact from ClinVar.
•Basic amino acid sequence information, Database of Single Nucleotide Polymorphism (dbSNP) IDs, and annotations from Uniprot and Interpro.
Annotations from the Variant Annotation Database are displayed in ArrayStar’s SNP Table and depend upon selections made in the Manage Columns dialog To narrow the list of variants to those of greatest interest, the Advanced Filtering dialog allows you to filter based on any of the annotations listed above (e.g., population genetics, functional impact, pathogenicity, etc.).