198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/human/hg19/gnomad.html src/hg/makeDb/trackDb/human/hg19/gnomad.html index ed4016e50bd..d6914d7ac79 100644 --- src/hg/makeDb/trackDb/human/hg19/gnomad.html +++ src/hg/makeDb/trackDb/human/hg19/gnomad.html @@ -1,128 +1,128 @@ <h2>Description</h2> <p> The tracks that are listed here contain data from unrelated individuals sequenced as part of various population-genetic and disease-specific <a target="_blank" href="https://gnomad.broadinstitute.org/about">studies</a> collected by the <a target="_blank" href="https://gnomad.broadinstitute.org/">Genome Aggregation Database (gnomAD)</a>. 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. Raw data from all studies have been reprocessed using a standardized pipeline and jointly variant-called process, which aims to increase consistency between projects. For more information on the processing pipeline and population annotations, see the following blog post <a target="_blank" href="https://macarthurlab.org/2017/02/27/the-genome-aggregation-database-gnomad">gnomAD</a>, <a target="_blank" href="https://macarthurlab.org/2018/10/17/gnomad-v2-1">gnomAD v2.1</a> and the 2.0.2 <a href="https://storage.googleapis.com/gnomad-public/release/2.0.2/README.txt" target="_blank">README</a>.</p> <p> The available data tracks are: <ul> <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadGenomes"><strong>Genome Variants (gnomAD Genomes)</strong></a> - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of <50 nucleotides (indels) of 15,708 unrelated individuals' genome sequences from the v2.1.1 release.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadExomes"><strong>Exome Variants (gnomAD Exomes)</strong></a> - Shows single nucleotide variants (SNVs) and small insertion/deletion variants of <50 nucleotides (indels) of 125,748 unrelated individuals' exome sequences from the v2.1.1 release.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadCoverage"><strong>Genome and Exome Sample Coverage (gnomAD Coverage)</strong></a> - Shows various read depth variant metrics calculated separately for exomes and genomes on a ~10% subset of the v2.0.2 samples.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadPext"><strong>Proportion Expression Across Transcript Scores (pext)</a></strong> - Shows exon-level expression for 53 GTEx tissues.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadStructuralVariants"><strong>Structural Variants (SV) (gnomAD Structural Variants)</strong></a> - Shows structural variants calls (variants >=50 nucleotides) from the gnomAD v2.1 release on 10,847 unrelated genomes.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadPLI"><strong>Predicted Constraint Metrics (gnomAD Constraint Metrics)</strong></a> - Contains metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadMpc"> <strong>Missense Deleteriousness Prediction by Constraint (MPC)</strong></a> - Regions of transcripts (not entire transcripts) that show enrichment of missense mutations.</li></ul> </p> <h2>Display Conventions</h2> <p> These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described <a target="_blank" href="https://genome.ucsc.edu/goldenPath/help/multiView.html">here</a>. Most gnomAD tracks contain multiple subtracks, corresponding to subsets of data. If a track contains many subtracks, only some -subracks will be displayed by default. The user can select which subtracks are displayed via the +subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details page. </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="http://hgdownload.soe.ucsc.edu/gbdb/$db/gnomAD/" target="_blank">download server</a>, subject to the conditions set forth by the gnomAD consortium (see below). Coverage values for the genome are in <a target="_blank" href="../goldenPath/help/bigWig.html">bigWig</a> files in the coverage/ subdirectory. Variant VCFs can be found in the vcf/ subdirectory.</p> <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> <p> More information about using and understanding the gnomAD data can be found in the <a target="_blank" href="https://gnomad.broadinstitute.org/faq">gnomAD FAQ</a> site. </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://opendatacommons.org/licenses/odbl/1.0/" target="_blank">ODC Open Database License (ODbL)</a> as described <a href="https://gnomad.broadinstitute.org/terms" target="_blank">here</a>. </p> <h2>References</h2> <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.ncbi.nlm.nih.gov/pubmed/27535533" target="_blank"> Analysis of protein-coding genetic variation in 60,706 humans</a>. <em>Nature</em>. 2016 Aug 18;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> <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://www.ncbi.nlm.nih.gov/pubmed/32461654" 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> Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/32461652" target="_blank"> A structural variation reference for medical and population genetics</a>. <em>Nature</em>. 2020 May;581(7809):444-451. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32461652" target="_blank">32461652</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334194/" target="_blank">PMC7334194</a> </p> <p> Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/32461655" target="_blank"> Transcript expression-aware annotation improves rare variant interpretation</a>. <em>Nature</em>. 2020 May;581(7809):452-458. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32461655" target="_blank">32461655</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334198/" target="_blank">PMC7334198</a> </p>