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/mgrb.html src/hg/makeDb/trackDb/human/mgrb.html index 9830c3165f2..b4ccb2f944d 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 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> 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>