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/alfaVcf.html src/hg/makeDb/trackDb/human/alfaVcf.html
index a7dea386bf3..388ce77359e 100644
--- src/hg/makeDb/trackDb/human/alfaVcf.html
+++ src/hg/makeDb/trackDb/human/alfaVcf.html
@@ -29,27 +29,27 @@
 
 <h2>Methods</h2>
 <p>
 The ALFA pipeline processes genotype data from approved, unrestricted dbGaP studies, including
 chip array, exome, and genomic sequencing data. Selected study data undergoes quality assurance
 and transformation to standard VCF format. Variants are converted to SPDI notation and normalized
 using VOCA, then aggregated, remapped, and clustered to existing dbSNP rs identifiers or assigned
 new ones. Sample ancestries are validated using GRAF-pop and assigned to 12 major populations.
 QC exclusions include variants and subjects with call rate &lt;95%, datasets failing Ancestry
 Informative Markers consistency checks, and array datasets with conflicting or flipped allele
 orientation.
 </p>
 <p>
 The ALFA R4 bigBed files (904M variants) were converted to VCF using a custom script, retaining
 the 163M variants with non-zero allele frequency (146M SNPs, 17M indels).
-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 the source files of the varFreqs track were converted.
+For some tracks, python scripts were also needed; these are available on <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>.
 </p>
 
 <h2>References</h2>
 <p>
 NCBI ALFA does not yet have a peer-reviewed primary publication. Cite the project as:
 Phan L, Jin Y, Zhang H, Qiang W, Shekhtman E, Shao D <em>et al</em>.
 <a href="https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/" target="_blank">
 ALFA: Allele Frequency Aggregator</a>.
 National Center for Biotechnology Information, U.S. National Library of Medicine, 10 March 2020.
 </p>