38bafc856320cf5360e0482faeee72b78f2ea963 lrnassar Tue May 5 14:13:30 2026 -0700 QA pass on varFreqs per-subtrack description pages: encode 3 plain emails, add target=_blank to 15 boilerplate REST API links, and add missing References sections (and Data Access on varFreqsAll). refs #36642 Mechanical fixes across 18 per-subtrack description pages: - Encoded 3 plain author/contact emails: pfeliciano@simonsfoundation.org (sfariSparkExomes), m.hobbs@garvan.org.au (mgrb), contact_npco@a-star.edu.sg (npm). - Added target="_blank" to 15 occurrences of the boilerplate "<a href=https://api.genome.ucsc.edu>REST API</a>" link across allofus, topmed, sfariSparkExomes, tommo60kjpn, alfaVcf, gasp, abraom, indigenomes, hrc, saudi, schema, sgdpFreq, gregor, hgdp1kFreq, colorsDbSnv. Added missing References sections: - allofus.html: All of Us Research Program 2024 Nature. - topmed.html: Taliun 2021 Nature. - alfaVcf.html: NCBI ALFA documentation citation (no peer-reviewed paper yet). - gregor.html: GREGoR R04 Methods document + consortium website (no flagship publication yet). - varFreqsAll.html: pointer to the supertrack's References section, plus tool citations (bcftools csq, Ensembl VEP). Added missing Data Access section on varFreqsAll.html explaining that the merged callset is not downloadable due to mixed source-data licensing, but can be reconstructed from the per-subtrack VCFs using the conversion scripts on GitHub. All 25 unique varFreqs description pages now have Description, Methods, Data Access, References. No non-ASCII characters and no inline event handlers across the set. diff --git src/hg/makeDb/trackDb/human/indigenomes.html src/hg/makeDb/trackDb/human/indigenomes.html index 87b91cbdda5..fd599135951 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 +For programmatic access, our <a href="https://api.genome.ucsc.edu" target="_blank">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/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>. </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>