TogoVar datasets

Human genome reference sequence

Variant datasets derived from individual genome data in Japanese Genotype-phenotype Archive (JGA)

Dataset name Version/Last update Sample size Number of detected variants Number of variants after the exclusion Author
JGA-NGS 2018/06/01 125 13,338,968 4,679,025 NBDC
JGA-SNP 2018/06/01 183,884 1,966,919 1,249,724 NBDC

Note that variants with 5 alternative alleles or less were excluded from JGA-NGS and JGA-SNP datasets.

Variant datasets generated by third parties

Dataset name Version/Last update Sample size Number of variants Number of variant sites Author
ClinVar 2019/06/24 — 443,213 — NCBI
Exome Aggregation Consortium (ExAC) Release 1 (2017/02/27) 60,706 10,195,872 9,362,319 Broad Institute
Human Genetic Variation Database (HGVD) Version 2.30 (2017/08/02) 1,208 554,461 501,556 Kyoto University
ToMMo 3.5KJPNv2 Allele Frequency Panel (3.5KJPN) v20181105open; Unfiltered 3,552 64,675,495 60,816,012 Tohoku Medical Megabank Organization

Note 1: TogoVar contains ClinVar variants only in the VCF file, GRCh37 positions of which were determined.

Note 2 : 3.5KJPNv2 consists of SNVs and INDELSs on Autosome, chrX (PAR1+PAR2+XTR) and chrMT. See Summary of ToMMo 3.5KJPNv2 (v20181105; Unfiltered).

Datasets other than those for variants

Dataset name Version/Last update Description Author
Colil 2018/01/29 Information on citation relationships in life sciences literature DBCLS
PubTator 2018/04/23 Information on papers in which the names of variants appear NCBI
TogoGenome hg19+Ensembl96 Various information on genomes DBCLS

Tools for data processing

Name Ver. Description Author
bcftools Normalize indels and split multiallelic sites into biallelic variants Genome Research Ltd.
BioReT ‐ Execute programs for variant discovery from NGS data in proper order Amelieff
Variant Effect Predictor (VEP) Ver.96 Add annotations like gene names or consequences to variants EMBL-EBI