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/saudi.html src/hg/makeDb/trackDb/human/saudi.html
index 177ef275165..70fc6f7c01e 100644
--- src/hg/makeDb/trackDb/human/saudi.html
+++ src/hg/makeDb/trackDb/human/saudi.html
@@ -15,37 +15,37 @@
 track name is <em>saudi</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 data were downloaded from
 <a href="https://figshare.com/articles/dataset/A_list_of_Saudi_Arabian_variants_and_their_allele_frequencies/28059686/1?file=51297884"
 target="_blank">Figshare</a> and converted to VCF.
 </p>
 
 <h2>Methods</h2>
 <p>
 Whole-genome sequencing of 302 Saudi Arabian individuals was performed on the Illumina HiSeq
 X Ten platform using TruSeq Nano DNA library preparation at 30x target coverage. Sequencing and
 initial bioinformatics processing were carried out by deCODE Genetics (Reykjav&iacute;k, Iceland).
-Reads were aligned to the GRCh38 reference genome using BWA 0.7.10. Per-sample variant calling
-was performed with GATK HaplotypeCaller, followed by joint genotyping using CombineGVCFs and
+Reads were aligned to the GRCh38 reference genome using BWA 0.7.10. Per-sample variants
+were called with GATK HaplotypeCaller, then jointly genotyped with CombineGVCFs and
 GenotypeGVCFs. Variant quality score recalibration (VQSR) was applied for both SNPs and indels.
 The final autosomal callset contains 25.5 million variants across the 302 individuals.
 </p>
 <p>
 The variant data were downloaded from
 <a href="https://figshare.com/articles/dataset/A_list_of_Saudi_Arabian_variants_and_their_allele_frequencies/28059686/1?file=51297884"
 target="_blank">Figshare</a> and converted to VCF format using a custom script.
-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; these 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>
 Malomane DK, Williams MP, Huber CD, Mangul S, Abedalthagafi M, Chiang CWK.
 <a href="https://doi.org/10.1101/2025.01.10.632500" target="_blank">
 Patterns of population structure and genetic variation within the Saudi Arabian population</a>.
 <em>bioRxiv</em>. 2025 Jan 13;.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39868174" target="_blank">39868174</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761371/" target="_blank">PMC11761371</a>
 </p>