We are excited to announce the NCBI Allele Frequency Aggregator (ALFA) Release 2 (version 20201027095038) as one of the largest and most comprehensive aggregated variant datasets with allele frequency available as open-access. This release contains 79 dbGaP studies that included 192 thousand subjects and 5.8 trillion combined genotypes that generated allele frequency for 904 million variants with 316 million novel ones, previously unknown in dbSNP (Build 154).
Tag: dbGaP Allele Frequency Aggregator (ALFA)
Two up-and-coming NCBI resources will be featured in videos, surveys and live events at the American Society for Human Genetics (ASHG) 2020 Annual Meeting. Come and watch on-demand videos in the CoLab Theater. Then, let us know what you think and how you do or might use these resources by either taking an online survey or joining us for the CoLab Live! Events on Thursday, October 29, 2020.
dbSNP human build 154, now available, includes new ALFA (Allele Frequency Aggregator) variants and allele frequency. This build contains over two billion Submitted SNP (ss) records and 730 million Reference SNP (rs) records.
New features include:
- dbSNP search now support HGVS and protein variant search
- RefSNP page linked to Litvar information
- Filter and facet to retrieve all SNPs with ALFA frequency
See the release notes for more information about what’s new in build 154.
NIH’s data sharing policy now allows unrestricted access to genomic summary results for data from NCBI’s Database of Genotypes and Phenotypes (dbGaP). Pooled allele frequency data from dbSNP and the dbGaP summary results are available as the new Allele Frequency Aggregator (ALFA) dataset. The ALFA dataset includes aggregated and harmonized array chip genotyping, exome, and genome sequencing data. The ALFA data are open access and freely available for you to incorporate into your workflows and applications from the dbSNP web pages (Figure 1), through FTP,and the Variation Services API. dbGaP currently has data for more than 2 million study subjects, approximately 1 million of whom have genotype data that is suitable for input into the ALFA dataset. The first release of ALFA contains data on about 100,000 subjects, and we hope to complete processing of data on the other 925,000 subjects within the next year. This volume and variety of data promises unprecedented opportunities to identify genetic factors that influence health and disease. Register to attend our April 22 webinar and read on to learn more.
Figure 1. ALFA allele frequencies for a variant (rs4988235) in the promotor of the lactase gene showing frequency differences across populations.
Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.
Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips
This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.