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/mgrb.html src/hg/makeDb/trackDb/human/mgrb.html index b4ccb2f944d..8a2c749745a 100644 --- src/hg/makeDb/trackDb/human/mgrb.html +++ src/hg/makeDb/trackDb/human/mgrb.html @@ -1,45 +1,45 @@ <h2>Description</h2> <p> The <a href="https://sgc.garvan.org.au/initiatives/mgrb/index.html" target="_blank">Australian Medical Genome Reference Bank (MGRB)</a> collected whole-genome sequencing data of 4,011 healthy elderly individuals who lived ≥70 years, to make sure that the dataset is depleted of damaging genetic variants. Age and sex summary graphs are available from <a href="https://sgc.garvan.org.au/initiatives/mgrb/index.html" target="_blank">the MGRB website</a>. </p> <h2>Data Access</h2> <p> Due to license restrictions, the data for this track cannot be downloaded from the UCSC Genome Browser. The Table Browser, Data Integrator, and download server are not available for this track. </p> <p> VCF access can be requested via a form from <a href="https://sgc.garvan.org.au/terms/mgrb/index.html" target="_blank">Sydney Genomics</a>. </p> <h2>Methods</h2> <p> The 4,011 MGRB samples underwent whole-genome sequencing on Illumina HiSeq X instruments at KCCG under ISO 15189 accreditation, using paired-end TruSeq DNA Nano libraries sequenced one lane per sample. Alignment of sequence reads to the hg38 reference genome assembly was with bwa 0.7.15-r1140. Variants were called following the Genome Analysis Toolkit (GATK) best practices procedure using GATK 4.1.4.0. A sites-only VCF with only passing variants (FILTER=PASS) was made with bcftools 1.20. </p> <p> -We received VCF files from m.hobbs@garvan.org.au via a transfer link and imported these VCFs. +We received VCF files from <A HREF="mailto:m.hobbs@garvan.org.au">m.hobbs@garvan.org.au</A><!-- above address is m.hobbs at garvan.org.au --> via a transfer link and imported these VCFs. 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> Lacaze P, Pinese M, Kaplan W, Stone A, Brion MJ, Woods RL, McNamara M, McNeil JJ, Dinger ME, Thomas DM. <a href="https://doi.org/10.1038/s41431-018-0279-z" target="_blank"> The Medical Genome Reference Bank: a whole-genome data resource of 4000 healthy elderly individuals. Rationale and cohort design</a>. <em>Eur J Hum Genet</em>. 2019 Feb;27(2):308-316. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30353151" target="_blank">30353151</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336775/" target="_blank">PMC6336775</a> </p>