Tag: Database of human genomic structural variation (dbVar)
NCBI’s database of structural variation, dbVar has a restructured FTP directory. The old directories can be found in archive.
Highlights include:
Refer to README.ftp for full details of the new GVF, VCF, TSV, and XML files.
RefSeq release 85 is now accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript, and protein data available, as of November 6, 2017, and contains 146,710,309 records, including 100,043,962 proteins, 20,905,608 RNAs, and sequences from 73,996 organisms. The release is provided in several directories as a complete dataset and as divided by logical groupings. See the RefSeq release notes for more information.
Starting in March 2018, SNP variation features will no longer be in RefSeq genome assembly records – chromosome and contig records with NC_, NT_, NW_ and AC_ accession prefixes. This change affects both the ASN.1 and flatfile records. Because the number of variants is already enormous and still growing, removing SNP features from these large genomic records will significantly reduce the size of RefSeq FTP files and make downloading and processing easier. We will continue to include SNPs on NG_-prefixed genomic records, and transcript (NM_, NR_, XM_, XR_) and protein (NP_, XP_, YP_) sequences.
Reminder: As of September 2017, NCBI has stopped accepting submissions for non-human SNPs in dbSNP and dbVar. RefSeq flatfiles will stop presenting non-human variant data in November 2017.
Subscribe to the refseq-announce listserv for regular updates on RefSeq.
Copy number variants (CNVs) from ExAC’s publication are now available at dbVar as nstd151. The data include approximately 50,000 CNV regions identified from 60,000 human exomes, providing a deep survey of common and rare copy number variation affecting protein-coding sequences in the human genome.
dbVar provides FTP files in VCF, GVF, and CSV formats, and include placements on GRCh37 as well as remapped placements on GRCh38. Tutorials for working with different formats are also available.
Follow the dbVar RSS feed for information on monthly releases.
RefSeq release 84 is now accessible online, via FTP and through NCBI’s programming utilities.
This full release incorporates genomic, transcript, and protein data available, as of September 11, 2017, and contains 140,627,690 records, including 95,563,598 proteins, 20,356,598 RNAs, and sequences from 72,965 organisms.
The release is provided in several directories as a complete dataset and as divided by logical groupings. See the RefSeq release notes for more information.
As of September 1, 2017, the dbSNP and dbVar databases have stopped accepting submissions for non-human organisms. Submissions for non-human variation will now be accepted by the European Variation Archive, one of our partners in the International Nucleotide Sequence Database (INSDC).
RefSeq release 83 is now accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript, and protein data available as of July 17, 2017, and contains 132,052,465 records, including 88,385,530 proteins, 19,634,664 RNAs, and sequences from 71,356 organisms. The release is provided in several directories as a complete dataset and as divided by logical groupings. More information about RefSeq release 83 is available in the release notes.
NCBI will phase out support for non-human organisms in the dbSNP and dbVar databases. These databases will stop accepting submissions for non-human SNPs in September 2017. The interactive websites for these databases and related NCBI services, including RefSeq flatfiles, will stop presenting non-human variant data in November 2017.
This blog post is directed toward people who use dbSNP and dbVar, particularly those who submit non-human data to the two databases.
dbSNP and dbVar archive, process, display and report information related to germline and somatic variations from multiple species. These two databases have grown rapidly as sequencing and other discovery technologies have evolved, and now contain nearly two billion variants from over 360 species.
Based on projected growth and the resources required to archive and distribute the data, continued support for all organisms will become unsustainable for NCBI in the near future. Therefore, NCBI will phase out support for all non-human organisms in dbSNP and dbVar, and will support only human variation.
Continue reading “Phasing out support for non-human genome organism data in dbSNP and dbVar”