dbVar, NCBI’s database of large-scale genetic variants, has a new track hub for viewing and downloading structural variation (SV) data in popular genome browsers. Initial tracks include Clinical and Common SV datasets. dbVar’s new track hub can be viewed using NCBI’s Genome Data Viewer through the “User Data and Track Hubs” feature (Figure 1) and other genome browsers by selecting “dbVar Hub” from the list of public tracks or by specifying the following URL.
https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt
Figure 1. Loading the dbVar track hub in the Genome Data Viewer. The Track Hubs feature on the left-hand column of the browser allow you to add the track by searching for it or by entering the direct URL. You can select the specific tracks — for example, “NCBI curated common SVs: All populations” — to load from the Configure Track Hubs dialog.
Figure 2. The Genome Data Viewer showing the region of chromosome 1 containing the mu class gluathione S-transferase gene family. The Common SV track for all populations shows many copy number variant regions for GSTM1 and GSTM2. Track display options for this view: Rendering options, All features are expanded; Feature linking, Show parent, not children.
The Clinical SV track contains all variants in ClinVar 50bp or greater in size, separated into Pathogenic and Non-pathogenic subtracks. Clinical variant data are updated every month when ClinVar releases new XML. The Common SV track displayed in the viewer in Figure 2 contains NCBI curated structural variants, a set derived from all the copy number variants (CNV) in dbVar with a reported allele frequency of 0.01 or greater, from studies of 100 or more individuals. Source data currently include gnomAD (nstd166), DECIPHER (nstd183), and 1000 Genomes (nstd214). The Common SV track has subtracks for the data sources as well as various human population subsets.
All dbVar track hub data are available on both GRCh38 and GRCh37 and will be kept up to date as more data become available.
We welcome your feedback and suggestions for improving this new resource.