aa61ebc800429515f9ced7e28f669c6042219f43 max Wed Mar 18 09:09:13 2026 -0700 varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 diff --git src/hg/makeDb/trackDb/human/tommo60kjpn.html src/hg/makeDb/trackDb/human/tommo60kjpn.html new file mode 100644 index 00000000000..3c89894d2c9 --- /dev/null +++ src/hg/makeDb/trackDb/human/tommo60kjpn.html @@ -0,0 +1,50 @@ +

Description

+An allele frequency panel based on short-read whole-genome sequencing analysis of 61,000 Japanese +individuals, produced by the +Tohoku Medical Megabank +Organization (ToMMo) at Tohoku University. The project includes other datatypes such as STRs, +long-read SVs and short-read CNVs. +

+ +

Data Access

+The data can be explored interactively with the +Table Browser or the +Data Integrator. +For programmatic access, our REST API can be used; the +track name is tommo60kjpn. +For bulk download, the VCF file can be obtained from +our download server. +

+The original data can also be downloaded from the jMorp website, specifically the +Downloads section. +

+ +

Methods

+Genomic DNA was obtained from peripheral blood, saliva, or cord blood samples. Sequencing was +performed on Illumina HiSeq 2500, HiSeq X Five, NovaSeq 6000, and MGI DNBSeq G400/T7 instruments. +Reads were aligned to the GRCh38 reference using BWA 0.7.15 or BWA-mem2 2.1. Alignments underwent +base quality score recalibration (BQSR) with the GATK BaseRecalibrator tool. SNV/indel calling was +performed using GATK HaplotypeCaller, followed by multisample joint genotyping with Sentieon +Genomics tools and variant quality score recalibration (VQSR) filtering. Related samples were +identified and removed using KING 2.3.1, resulting in the final allele frequency panel. +

+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. +

+ +

References

+Tadaka S, Kawashima J, Hishinuma E, Saito S, Okamura Y, Otsuki A, Kojima K, Komaki S, Aoki Y, Kanno +T et al. + +jMorp: Japanese Multi-Omics Reference Panel update report 2023. +Nucleic Acids Res. 2024 Jan 5;52(D1):D622-D632. +PMID: 37930845; PMC: PMC10767895 +