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/topmed.html src/hg/makeDb/trackDb/human/topmed.html
index d67f8a75e61..cf4f6ebda7c 100644
--- src/hg/makeDb/trackDb/human/topmed.html
+++ src/hg/makeDb/trackDb/human/topmed.html
@@ -32,29 +32,29 @@
 Genetics, University of Michigan), comprising: (1) per-sample candidate variant detection with
 <code>vt discover2</code> and normalization with <code>vt normalize</code>; (2) cross-sample variant site
 consolidation using <code>cramore vcf-merge-candidate-variants</code>; (3) joint genotyping across all
 samples; and (4) variant filtering using a Support Vector Machine (SVM) classifier
 (libsvm) trained on positive labels derived from HapMap 3.3 and 1000 Genomes Omni2.5
 array sites, and negative labels derived from Mendelian-inconsistent variants identified
 within the cohort's pedigree structure using <code>vt milk-filter</code>. Sample-level quality
 control included estimation of DNA contamination, genetic ancestry, and biological sex
 using <code>cramore cram-verify-bam</code> (verifyBamID2) and relative X/Y chromosomal depth. Full
 methods for TOPMed freeze 10 are available on the
 <a href="https://topmed.nhlbi.nih.gov/topmed-whole-genome-sequencing-methods-freeze-10"
    target="_blank">TOPMed WGS Methods page</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.
+Documentation on how all source files of the varFreqs track were converted is 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>
 Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM,
 Kang HM <em>et al</em>.
 <a href="https://doi.org/10.1038/s41586-021-03205-y" target="_blank">
 Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program</a>.
 <em>Nature</em>. 2021 Feb;590(7845):290-299.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33568819" target="_blank">33568819</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875770/" target="_blank">PMC7875770</a>
 </p>