62b1428915cc2c8b9acbf46a86c1248833257efe mspeir Mon Nov 17 18:50:32 2025 -0800 changing rest of genome-source references to github, refs #34485 diff --git src/hg/makeDb/trackDb/human/dbSnp155Composite.html src/hg/makeDb/trackDb/human/dbSnp155Composite.html index 4f3bc79cf78..0dd59a48626 100644 --- src/hg/makeDb/trackDb/human/dbSnp155Composite.html +++ src/hg/makeDb/trackDb/human/dbSnp155Composite.html @@ -502,36 +502,36 @@ that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline, web infrastructure, and download files. (Holmes et al.) The same challenges of exponential growth affected UCSC's presentation of dbSNP variants, so we have taken the opportunity to change our internal representation and import pipeline. Most notably, flanking sequences are no longer provided by dbSNP, because most submissions have been genomic variant calls in VCF format as opposed to independent sequences.

We downloaded JSON files available from dbSNP at https://ftp.ncbi.nlm.nih.gov/snp/archive/b155/JSON/, extracted a subset of the information about each variant, and collated it into a bigBed file using the -bigDbSnp.as schema with the information necessary for filtering and displaying the variants, as well as a separate file containing more detailed information to be displayed on each variant's details page -(dbSnpDetails.as schema).

Data Access

Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry.

Since dbSNP has grown to include over 1 billion variants, the size of the All dbSNP (155) subtrack can cause the Table Browser and Data Integrator to time out, leading to a blank page or truncated output, unless queries are restricted to a chromosomal region, to particular defined regions, to a specific set of rs# IDs (which can be pasted/uploaded into the Table Browser),