9bfd58221b1539193cb7f0a317b4e959c1c7e49a
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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/kova.html src/hg/makeDb/trackDb/human/kova.html
index a31dbab8906..80b39329156 100644
--- src/hg/makeDb/trackDb/human/kova.html
+++ src/hg/makeDb/trackDb/human/kova.html
@@ -10,48 +10,48 @@
<h2>Data Access</h2>
<p>
Due to license restrictions, the data for this track cannot be downloaded from the UCSC
Genome Browser. The Table Browser, Data Integrator, and download server are not available
for this track.
</p>
<p>
TSV data can be requested on the <a href="https://www.kobic.re.kr/kova/downloads"
target="_blank">KOVA Downloads</a> website. Our GitHub repo contains a script that
converts this format to VCF.
</p>
<h2>Methods</h2>
<p>
-Raw reads were aligned to the GRCh38+decoy reference using BWA-MEM v0.7.17 with default
-parameters, followed by duplicate marking and coordinate sorting with MarkDuplicatesSpark, and base
-quality score recalibration using BQSRPipelineSpark in GATK v4.1.3.0; mapping quality control
+Raw reads were aligned to the GRCh38+decoy reference with BWA-MEM v0.7.17 with default
+parameters. Duplicates were marked and coordinates sorted with MarkDuplicatesSpark, then base
+quality scores were recalibrated with BQSRPipelineSpark in GATK v4.1.3.0. Mapping quality control
metrics were generated with Qualimap v2.2.1. Single-nucleotide variants and small
-insertions/deletions were called per sample using GATK HaplotypeCaller in GVCF mode (-ERC GVCF), and
-joint genotyping was performed by creating a GenomicsDB with GenomicsDBImport and following GATK
-Best Practices, including variant quality score recalibration (VQSR) retaining 99.7% of true SNVs
+insertions/deletions were called per sample with GATK HaplotypeCaller in GVCF mode (-ERC GVCF), and
+joint genotyping was performed by creating a GenomicsDB with GenomicsDBImport and followed GATK
+Best Practices. Variant quality score recalibration (VQSR) retained 99.7% of true SNVs
and 99.0% of true indels based on training sets (workflow detailed in Supplementary Fig. 1).
Downstream analyses followed a modified version of the gnomAD quality-control framework and were
-primarily conducted using Hail; after merging WES and WGS data in Hail, multiallelic variants and
-variants with genotype quality <20, read depth <10, allelic balance <0.2, or overlapping
+primarily conducted with Hail. After WES and WGS data were merged in Hail, multiallelic variants and
+variants with genotype quality <20, read depth <10, allelic balance <0.2, or overlap with
low-complexity regions were excluded.
</p>
<p>
-At UCSC, V7 of the TSV.gz was obtained from the KOVA staff by email and converted to VCF. It is not
-available for download from our site but can be requested from the KOVA website.
-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>.
+At UCSC, V7 of the TSV.gz was obtained from the KOVA staff by email and converted to VCF. The file is not
+available for download from our site, but can be requested from the KOVA website.
+The <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/varFreqs.txt" target="_blank">makeDoc file</a> for the varFreqs track documents how all source files were converted.
+Python scripts used for some of the tracks are available on <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/scripts/varFreqs" target="_blank">GitHub</a>.
</p>
<h2>Credits</h2>
<p>
Thanks to Insu Jang and the KOVA director for providing variant frequencies in TSV format.
</p>
<h2>References</h2>
<p>
Lee J, Lee J, Jeon S, Lee J, Jang I, Yang JO, Park S, Lee B, Choi J, Choi BO <em>et al</em>.
<a href="https://doi.org/10.1038/s12276-022-00871-4" target="_blank">
A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East
Asian population</a>.
<em>Exp Mol Med</em>. 2022 Nov;54(11):1862-1871.
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36323850" target="_blank">36323850</a>; PMC: <a