383da828477aad2b3c6053880a64fdbfc2a00cd9 max Thu Mar 19 02:30:41 2026 -0700 Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/indigenomes.html src/hg/makeDb/trackDb/human/indigenomes.html index 2a07cf8c13a..87b91cbdda5 100644 --- src/hg/makeDb/trackDb/human/indigenomes.html +++ src/hg/makeDb/trackDb/human/indigenomes.html @@ -1,57 +1,57 @@ <h2>Description</h2> <p> <a href="https://clingen.igib.res.in/indigen/" target="_blank">IndiGenomes</a> provides whole genome sequencing data of 1,029 healthy Indian individuals under the pilot phase of the "IndiGen" program. Only the allele frequency is available from this project. The website also provides SV call and Alu insertion VCFs. </p> <h2>Data Access</h2> <p> The data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, our <a href="https://api.genome.ucsc.edu">REST API</a> can be used; the track name is <em>indigenomes</em>. For bulk download, the VCF file can be obtained from -<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/varFreqs/" target="_blank">our download server</a>. +<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/" target="_blank">our download server</a>. </p> <p> The original data can also be downloaded from the <a href="https://clingen.igib.res.in/indigen/" target="_blank">IndiGen website</a>. </p> <h2>Methods</h2> <p> Genomic DNA was extracted from 5 ml of peripheral blood collected via venipuncture from 1,029 self-declared healthy Indian individuals representing diverse geographic, ethnic, and linguistic groups, using the salting-out method. Whole-genome libraries were prepared using the TruSeq DNA PCR-free library preparation kit (Illumina). Sequencing was performed on the Illumina NovaSeq 6000 platform with 150×2 bp paired-end reads targeting ≥30× mean coverage. Alignment to the GRCh38 reference genome, post-processing, and default quality-filtered variant calling were performed end-to-end on the Illumina DRAGEN v3.4 Bio-IT platform, which uses field-programmable gate array (FPGA) logic for high-throughput processing. This yielded a compendium of 55,898,122 single allelic genetic variants (SNVs and indels), of which 32.23% were unique to the Indian samples and absent from global reference databases. Variants were annotated using ANNOVAR with RefGene, and allele frequencies were cross-referenced against gnomAD v3, 1000 Genomes, ExAC, ESP6500, and the Greater Middle East Variome Project. The dataset is accessible via the <a href="https://clingen.igib.res.in/indigen/" target="_blank">IndiGenomes database</a> (Jain, Bhoyar, Scaria, Sivasubbu & the IndiGen Consortium, <a href="https://doi.org/10.1093/nar/gkaa923" target="_blank"><em>Nucleic Acids Research</em> 2021</a>). </p> <p> -We provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target=_blank>makeDoc file</a> of the track. -For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target=_blank>Github</a>. +We provide documentation that indicates how all source files of the varFreqs track were converted in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> of the track. +For some tracks, python scripts were necessary and are also available from <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>. </p> <h2>References</h2> <p> Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B <em>et al</em>. <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkaa923" target="_blank"> IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes</a>. <em>Nucleic Acids Res</em>. 2021 Jan 8;49(D1):D1225-D1232. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33095885" target="_blank">33095885</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778947/" target="_blank">PMC7778947</a> </p>