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/gnomadV4.1.html src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html index b4efb3a7161..39d62f689aa 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html +++ src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html @@ -1,154 +1,158 @@ <h2>Description</h2> <p> GnomAD 4 used the whole-genome data from gnomAD 3 and added more exomes. -The current v4.1 release includes a fix for the allele number +The v4.1 release included a fix for the allele number <a target="_blank" href="https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/">issue</a>. -The v4.1 track shows variants from 807,162 individuals, including 730,947 +The current v4.1.1 release, from March 30, 2026, revises the LOFTEE END_TRUNC GERP distance +threshold from -58.0 to 0.0. This reclassifies about 79,920 predicted loss-of-function (pLoF) +variants from high-confidence to low-confidence. For more information, see the related <a +target="_blank" href="https://gnomad.broadinstitute.org/news/2026-03-gnomad-v4-1-1/">blog post</a>. +</p> +<p> +The track shows variants from 807,162 individuals, including 730,947 exomes and 76,215 genomes. This includes the 76,156 genomes from the gnomAD v3.1.2 release as well -as new exome data from 416,555 UK Biobank individuals. For more detailed information on gnomAD -v4.1, see the related <a target="_blank" -href="https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/">blog post</a>. +as exome data from 416,555 UK Biobank individuals. </p> <h2>Display Conventions and Configuration</h2> <p> Following the conventions on the gnomAD browser, items are shaded according to their Annotation type: <table class="stdTbl"> <tr><td>pLoF</td><td width="50px" style="background: rgb(255,32,0)"></td></tr> <tr><td>Missense</td><td width="50px" style="background: rgb(247,189,0)"></td></tr> <tr><td>Synonymous</td><td style="background: rgb(4,255,0)"></td></tr> <tr><td>Other</td><td style="background: rgb(95,95,95)"></td></tr> </table> </p> <p> Mouse hover on an item will display the following details about each variant:</p> <ul> <li>Position</li> <li>Total Allele Frequency (TotalAF)</li> <li>Genes</li> <li>Annotation</li> <li>FILTER tags from VCF (FILTER)</li> <li>Population with maximum AF (PopMaxAF)</li> <li>Homozygous Individuals</li> <li>Homozygous Individuals in XX samples (chrX and chrY only)</li> <li>Hemizygous Individuals (chrX and chrY only)</li> </ul> <p> Clicking on an item will display additional details on the variant, including a population frequency table showing allele count in each sub-population. </p> <h4>Label Options</h4> <p> To maintain consistency with the gnomAD website, variants are by default labeled according to their chromosomal start position followed by the reference and alternate alleles, for example "chr1-1234-T-CAG". dbSNP rsID's are also available as an additional label, if the variant is present in dbSnp. </p> <h4>Filtering Options</h4> <p> Three filters are available for this track: </p> <ul> <li>FILTER: Used to exclude/include variants that failed Random Forest (RF), Inbreeding Coefficient (Inbreeding Coeff), or Allele Count (AC0) filters. The PASS option is used to include/exclude variants that pass all of the RF, InbreedingCoeff, and AC0 filters, as denoted in the original VCF. <li>Annotation type: Used to exclude/include variants that are annotated as Probability Loss of Function (pLoF), Missense, Synonymous, or Other, as annotated by VEP. <li>Variant Type: Used to exclude/include variants according to the type of variation, as annotated by VEP. </ul> There is one additional configurable filter on the minimum minor allele frequency. <h2>UCSC Methods</h2> <p> -The gnomAD v4.1 data is unfiltered.</p> +The gnomAD v4.1.1 data is unfiltered.</p> <p> For the full steps used to create the gnomAD tracks at UCSC, please see the <a href="https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/doc/hg38/gnomad.txt" target="_blank">hg38 gnomad makedoc</a>. </p> <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a target="_blank" href="../cgi-bin/hgTables"> Table Browser</a>, or the <a target="_blank" href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our <a target="_blank" href="/goldenPath/help/api.html">REST API</a>, and the genome annotations are stored in files that can be downloaded from our <a -href="https://hgdownload.soe.ucsc.edu/gbdb/$db/gnomAD/v4.1/" target="_blank">download server</a>, subject +href="https://hgdownload.soe.ucsc.edu/gbdb/$db/gnomAD/v4.1.1/" target="_blank">download server</a>, subject to the conditions set forth by the gnomAD consortium (see below).</p> <p> The underlying bigBed only contains enough information necessary to use the track in the browser. The extra data like VEP annotations and CADD scores are available in the -<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/gnomAD/v4.1/">same directory</a> +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/gnomAD/v4.1.1/">same directory</a> as the bigBed but in the files <em>details.tab.gz</em> and <em>details.tab.gz.gzi</em>. The details.tab.gz contains the gzip compressed extra data in JSON format, and the .gzi file is available to speed searching of this data. Each variant has an associated md5sum in the name field of the bigBed which can be used along with the _dataOffset and _dataLen fields to get the associated external data. For example:</p> <pre> # find an item of interest, the last two fields are _dataOffset and _dataLen: bigBedToBed genomes.bb stdout | head -4 | tail -1 chr1 12416 12417 854246d79dc5d02dcdbd5f5438542b6e [..omitted..] 67293 902 # use _dataOffset and _dataLen (add one to _dataLen for the newline character): -bgzip -b 67293 -s 903 gnomad.v4.1.genomes.details.tab.gz +bgzip -b 67293 -s 903 gnomad.v4.1.1.genomes.details.tab.gz 854246d79dc5d02dcdbd5f5438542b6e {"DDX11L1": {"cons": ["non_coding_transcript_variant"... </pre> <p> The data can also be found directly from the gnomAD <a target="_blank" href="https://gnomad.broadinstitute.org/downloads">downloads page</a>. Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">mailing list archives</a> for questions, or our <a target="_blank" href="../FAQ/FAQdownloads.html#download36">Data Access FAQ</a> for more information.</p> <h2>Credits</h2> <p> Thanks to the <a href="https://gnomad.broadinstitute.org/about" target="_blank">Genome Aggregation Database Consortium</a> for making these data available. The data are released under the <a href="https://creativecommons.org/publicdomain/zero/1.0/" target="_blank">Creative Commons Zero Public Domain Dedication</a> as described <a href="https://gnomad.broadinstitute.org/policies" target="_blank">here</a>. </p> <p> Please note that some annotations within the provided files may have restrictions on usage. See <a href="https://gnomad.broadinstitute.org/policies" target="_blank">here</a> for more information. </p> <h2>References</h2> <p> Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD <em>et al</em>. <a href="https://doi.org/10.1038/s41586-023-06045-0" target="_blank"> A genomic mutational constraint map using variation in 76,156 human genomes</a>. <em>Nature</em>. 2024 Jan;625(7993):92-100. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38057664" target="_blank">38057664</a> </p> <p> Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP <em>et al</em>. <a href="https://doi.org/10.1038/s41586-020-2308-7" target="_blank"> The mutational constraint spectrum quantified from variation in 141,456 humans</a>. <em>Nature</em>. 2020 May;581(7809):434-443. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32461654" target="_blank">32461654</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334197/" target="_blank">PMC7334197</a> </p> <p> Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB <em>et al</em>. <a href="https://www.nature.com/articles/nature19057" target="_blank">Analysis of protein-coding genetic variation in 60,706 humans</a>. <em>Nature</em>. 2016 Aug 17;536(7616):285-91. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27535533" target="_blank">27535533</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018207/" target="_blank">PMC5018207</a> </p>