SNV Frequencies Japan ToMMo 61k WGS Track Settings
Version: 2025-06-16 Assembly: Human Dec. 2013 (GRCh38/hg38)
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 with KING 2.3.1 to produce the final allele frequency panel.
The makeDoc file for this track describes how all source files of the varFreqs track were converted.
For some tracks, python scripts were needed and are available from GitHub.