9bfd58221b1539193cb7f0a317b4e959c1c7e49a
max
  Thu May 21 01:00:45 2026 -0700
varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/gasp.html src/hg/makeDb/trackDb/human/gasp.html
index 9a47fc8317c..62ee1ecc359 100644
--- src/hg/makeDb/trackDb/human/gasp.html
+++ src/hg/makeDb/trackDb/human/gasp.html
@@ -1,56 +1,56 @@
 <h2>Description</h2>
 <p>
 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" target="_blank">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/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&times;100 bp or 2&times;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
 &sim;65 million variants across 1,739 individuals from 219 populations.
 </p>
 <p>
 The upstream callset is on GRCh37. We lifted it to hg38 using
 <a href="https://crossmap.sourceforge.net/" target="_blank">CrossMap</a> and the UCSC
 <tt>hg19ToHg38</tt> chain file. After lifting, variants that landed on alt, random, fix, or
 unplaced contigs were dropped, and the result was sorted and indexed with tabix.
 </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>.
+The <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> documents how all source files of the varFreqs track were converted.
+For some tracks, python scripts were needed 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>