TogoVar Downloadable data for GRCh38

Last Updated: 2024/12/3

## Frequency data

For each dataset or subgroup, a VCF file containing allele counts, allele frequencies, and genotype counts is available
Visit https://grch38.togovar.org/doc/datasets for the description of each dataset.

List of datasets and subgroups
-----------------

1.GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel 

vcf/gem_j_wga: total count of GEM Japan Whole Genome Aggregation (GEM-J WGA) Panel 


2. Genome Aggregation Database (gnomAD) exomes

vcf/gnomad_exomes/all: Total count of the subpopulations below
vcf/gnomad_exomes/afr: African/African American
vcf/gnomad_exomes/amr: Admixed American
vcf/gnomad_exomes/asj: Ashkenazi Jewish
vcf/gnomad_exomes/eas: East Asian
vcf/gnomad_exomes/fin: European (Finnish)
vcf/gnomad_exomes/mid: Middle Eastern
vcf/gnomad_exomes/nfe: European (non-Finnish)
vcf/gnomad_exomes/remaining: Remaining individuals
vcf/gnomad_exomes/sas: South Asian


3. Genome Aggregation Database (gnomAD) genomes 

vcf/gnomad_genomes/all: Total count of the subpopulations below 
vcf/gnomad_genomes/afr: African/African American
vcf/gnomad_genomes/ami: Amish 
vcf/gnomad_genomes/amr: Admixed American
vcf/gnomad_genomes/asj: Ashkenazi Jewish
vcf/gnomad_genomes/eas: East Asian
vcf/gnomad_genomes/fin: European (Finnish)
vcf/gnomad_genomes/mid: Middle Eastern
vcf/gnomad_genomes/nfe: European (non-Finnish)
vcf/gnomad_genomes/remaining: Remaining individuals
vcf/gnomad_genomes/sas: South Asian


4. JGA-SNP dataset: aggregated SNP-chip data in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA). 

vcf/jga_snp: Total count of JGA-SNP
vcf/jga_snp/bbj_riken: JGA-SNP dataset aggregated by disease and sex for 45 diseases.


5. JGA-WES dataset: reanalyzing individual-level exome sequence data in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA)

vcf/jga_wes: Total count of JGA-WES


6. JGA-WGS dataset: reanalyzing individual-level whole genome sequence data in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA)

vcf/jga_wgs: Total count of JGA-WGS


7. National Center Biobank Network (NCBN)  

vcf/ncbn/all: Total count of NCBN and 1KGP samples

7.1 Samples collected by the National Center BioBank Network (NCBN) 
vcf/ncbn/jpn: Total count of the subpopulations below   
vcf/ncbn/jpn.hondo:  Mainland of Japan 
vcf/ncbn/jpn.ryukyu: Ryukyu island of Japan

7.2 1000 Genomes Project (1KGP) samples, for which joint-calling with the NCBN samples was performed. 
vcf/ncbn/acb: African Caribbean in Barbados 
vcf/ncbn/asw: African Ancestry in SW USA
vcf/ncbn/beb: Bengali in Bangladesh 
vcf/ncbn/cdx: Chinese Dai in Xishuangbanna, China
vcf/ncbn/ceu: Utah residents (CEPH) with Northern and Western European ancestry
vcf/ncbn/chb: Han Chinese in Beijing, China
vcf/ncbn/chs: Han Chinese South
vcf/ncbn/clm: Colombian in Medellín, Colombia
vcf/ncbn/esn: Esan in Nigeria
vcf/ncbn/fin: Finnish in Finland
vcf/ncbn/gbr: British From England and Scotland
vcf/ncbn/gih: Gujarati Indians in Houston, Texas, USA
vcf/ncbn/gwd: Gambian in Western Division – Mandinka
vcf/ncbn/ibs: Iberian Populations in Spain
vcf/ncbn/itu: Indian Telugu in the U.K.
vcf/ncbn/jpt: Japanese in Tokyo, Japan
vcf/ncbn/khv: Kinh in Ho Chi Minh City, Vietnam
vcf/ncbn/lwk: Luhya in Webuye, Kenya
vcf/ncbn/msl: Mende in Sierra Leone
vcf/ncbn/mxl: Mexican Ancestry in Los Angeles CA USA
vcf/ncbn/pel: Peruvian in Lima Peru
vcf/ncbn/pjl: Punjabi in Lahore, Pakistan
vcf/ncbn/pur: Puerto Rican in Puerto Rico
vcf/ncbn/stu: Sri Lankan Tamil in the UK
vcf/ncbn/tsi: Toscani in Italia
vcf/ncbn/yri: Yoruba in Ibadan, Nigeria


8. ToMMo 54KJPN Allele Frequency Panel (54KJPN)
vcf/tommo: Total count of ToMMo 54KJPN