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 $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/gasp.html src/hg/makeDb/trackDb/human/gasp.html index ba30bc28f05..8efa4f255bb 100644 --- src/hg/makeDb/trackDb/human/gasp.html +++ src/hg/makeDb/trackDb/human/gasp.html @@ -3,48 +3,48 @@ The <a href="https://www.genomeasia100k.org/" target="_blank">GenomeAsia 100K</a> project aims to sequence 100,000 Asian individuals. This pilot release (GAsP) contains whole-genome sequencing data of 1,739 individuals from 219 population groups across Asia. Frequencies are broken down by Northeast Asian, Southeast Asian, and South Asian ancestry groups. The data is split into two subtracks: substitutions and indels. </p> <h2>Data Access</h2> <p> The data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, our <a href="https://api.genome.ucsc.edu">REST API</a> can be used; the track name is <em>gasp</em>. For bulk download, the VCF file can be obtained from -<a href="http://hgdownload.soe.ucsc.edu/gbdb/$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 VCFs are also available from the <a href="https://browser.genomeasia100k.org/#tid=download" target="_blank">GenomeAsia 100K website</a>. No license nor login is required. </p> <h2>Methods</h2> <p> Samples were sequenced on Illumina HiSeq 2500, HiSeq 4000, and HiSeq X Ten instruments with 2×100 bp or 2×150 bp paired-end reads at an average depth of 36x. Reads were aligned to GRCh37 using BWA-MEM. Duplicate reads were marked with SAMBLASTER and sorted with Sambamba. Per-sample variant calling was performed with GATK HaplotypeCaller in GVCF mode, followed by joint genotyping with GenotypeGVCFs. Variant quality score recalibration (VQSR) was applied at a 99% sensitivity tranche for both SNPs and indels. Sample-level QC included contamination checks with verifyBamID and sex concordance verification. The final callset contains ∼65 million variants across 1,739 individuals from 219 populations. </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> GenomeAsia100K Consortium. <a href="https://doi.org/10.1038/s41586-019-1793-z" target="_blank"> The GenomeAsia 100K Project enables genetic discoveries across Asia</a>. <em>Nature</em>. 2019 Dec;576(7785):106-111. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31802016" target="_blank">31802016</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054211/" target="_blank">PMC7054211</a> </p>