10db3769dd9edfa38ac8d900ca400fdfb514d9a7 gperez2 Wed Jul 29 22:41:46 2026 -0700 An in-place update for gnomad v4.1 to v4.1.1 that swaps bigDataUrl, labels, dataVersion, detailsTabUrls, search descriptions, and removes the alpha-only gnomadVariantsV4.1.1 composite. Updates to gnomad.html, gnomadV4.1.html, and gnomadPLI.html regarding the addition of the gnomad v4.1.1 data, refs #37351 diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.html src/hg/makeDb/trackDb/human/hg38/gnomad.html index fbcf956d017..88aa93d0db9 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomad.html +++ src/hg/makeDb/trackDb/human/hg38/gnomad.html @@ -2,38 +2,38 @@ <p> The <a target="_blank" href="https://gnomad.broadinstitute.org/">Genome Aggregation Database (gnomAD)</a> is a resource developed by an international coalition of investigators at the Broad Institute and collaborating institutions, with the goal of aggregating and harmonizing exome and whole-genome sequencing data from large-scale sequencing projects spanning disease-specific cohorts and population genetics studies. Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. For each variant, gnomAD provides allele frequencies stratified by genetic ancestry group, alongside quality metrics such as depth of coverage and genotype quality scores. The database also supplies sequencing coverage, structural variants, CNVs, and short tandem repeats. Additionally, gnomAD provides non-coding constraint and gene-level constraint metrics — including pLI scores, observed/expected (oe) ratios, and LOEUF values — that quantify intolerance to loss-of-function variation and are widely used to prioritize candidate disease genes. The most -current release on hg38 is v4.1, but the older v3 and v2 versions are also available. +current release on hg38 is v4.1.1, but the older v3 and v2 versions are also available. </p> <p> The available data tracks are: <ul> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariantsV4.1#TRACK_HTML"><strong>gnomAD -v4.1</strong></a> — Shows single nucleotide variants (SNVs) and small insertion/deletion +v4.1.1</strong></a> — Shows single nucleotide variants (SNVs) and small insertion/deletion variants of 807,162 individuals, including 730,947 exomes and 76,215 genomes.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3_1_1#TRACK_HTML"><strong>gnomAD v3.1.1</strong></a> — Shows variants from 76,156 whole genomes (and no exomes), all mapped to GRCh38/hg38.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3_1#TRACK_HTML"><strong>Deprecated: gnomAD v3.1</strong></a> — Same underlying data as v3.1.1 with older annotations. Do not use; will be removed soon.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3#TRACK_HTML"><strong>gnomAD v3</strong></a> — Shows variants from 71,702 whole genomes from the v3.0 release.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariantsV2#TRACK_HTML"><strong>gnomAD v2</strong></a> — Shows variants from 125,748 exomes and 15,708 whole genomes, lifted from GRCh37/hg19 to GRCh38/hg38.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadConstraint#TRACK_HTML"><strong>gnomAD Mut Constraint</strong></a> — Shows the reduced variation caused by purifying natural selection for 1kbp windows across the genome (based on v3.1.2).</li>