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 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 diff --git src/hg/makeDb/trackDb/human/mgrb.html src/hg/makeDb/trackDb/human/mgrb.html index 8a2c749745a..1dc19f7774c 100644 --- src/hg/makeDb/trackDb/human/mgrb.html +++ src/hg/makeDb/trackDb/human/mgrb.html @@ -1,45 +1,45 @@
Description

The Australian Medical Genome Reference Bank (MGRB) collected whole-genome sequencing data of 4,011 healthy -elderly individuals who lived ≥70 years, to make sure that the dataset is depleted of damaging -genetic variants. Age and sex summary graphs are available from +elderly individuals who lived ≥70 years, so the dataset is depleted of damaging genetic +variants. Age and sex summary graphs are available from the MGRB website.

Data Access

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.

VCF access can be requested via a form from Sydney Genomics.

Methods

The 4,011 MGRB samples underwent whole-genome sequencing on Illumina HiSeq X instruments at KCCG -under ISO 15189 accreditation, using paired-end TruSeq DNA Nano libraries sequenced one lane per -sample. Alignment of sequence reads to the hg38 reference genome assembly was with bwa 0.7.15-r1140. -Variants were called following the Genome Analysis Toolkit (GATK) best practices procedure using -GATK 4.1.4.0. A sites-only VCF with only passing variants (FILTER=PASS) was made with bcftools 1.20. +under ISO 15189 accreditation, with paired-end TruSeq DNA Nano libraries sequenced one lane per +sample. Sequence reads were aligned to the hg38 reference genome assembly with bwa 0.7.15-r1140. +Variants were called with GATK 4.1.4.0 following the Genome Analysis Toolkit (GATK) best practices +procedure. A sites-only VCF with only passing variants (FILTER=PASS) was made with bcftools 1.20.

-We received VCF files from m.hobbs@garvan.org.au via a transfer link and imported these VCFs. -We provide documentation that indicates how all source files of the varFreqs track were converted in the makeDoc file of the track. -For some tracks, python scripts were necessary and are also available from GitHub. +We received VCF files from m.hobbs@garvan.org.au via a transfer link and imported them. +The makeDoc file of the track documents how all source files of the varFreqs track were converted. +For some tracks, python scripts were needed; these are available from GitHub.

References

Lacaze P, Pinese M, Kaplan W, Stone A, Brion MJ, Woods RL, McNamara M, McNeil JJ, Dinger ME, Thomas DM. The Medical Genome Reference Bank: a whole-genome data resource of 4000 healthy elderly individuals. Rationale and cohort design. Eur J Hum Genet. 2019 Feb;27(2):308-316. PMID: 30353151; PMC: PMC6336775