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We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000220

Type of data
WGS for 1,026 individuals
Access criteria
Controlled-access (Type I)
Total data volume
75.1 TB
File formats
  • FASTQ
  • VCF
  • HTML
Research
hum0014
Date published
2020-09-28
Date modified
2022-08-23
DDBJ Search
JGAD000220 (opens in a new tab)
JGA Study
JGAS000114 (opens in a new tab)

Analysis method

WGS

Materials and participants
1,026 individuals
  • Health status
    Affected
  • Subject count
    1026 (Individual)
  • Cohort
    BioBank Japan
Sample description
DNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq Nano DNA Library Prep Kit
Fragmentation
Ultrasonic fragmentation
Platform
Illumina HiSeq 2500
Read type
Paired-end
Read length
160 bp
Reference genome
GRCh37
Mapping
BWA mem 0.7.12
Read deduplication
Picard 2.10.6
Realignment and base quality recalibration
GATK 3.7
Mapping quality
Reads with MAPQ<20 were excluded at variant calling with GATK 3.7 HaplotypeCaller
QC and filtering
Data with bad base quality and high %GC content were removed.
Alignment:
Data matched for the following conditions were removed.
- Low mapping rate
- Different insert size
- Gender information mismatch between meta-data and genotype data
- Suspected sex chromosome aberration
Genotyping:
GATK's best practices include a variant filtering step following Variant Quality Score Recalibration (VQSR)
- DP/GP (DP < 5, GQ < 20, DP > 60, GQ < 95)
- Heterozygosity (F>=0.05)
- Hardy-Weinberg equilibrium (p < 10^-6)
- Repeat & Low Complexity
Principal Component Analysis (PCA):
PCA was performed with individuals included in the 1000 genomes project and outliers from Japanese cluster were removed.

After these filtering steps, variants located in the regions listed as the HighConfidenceRegion (Genome-In-A-Bottle project) were flagged.
Analysis method
GATK 3.7 HaplotypeCaller
Coverage (depth)
31.8x
Variant count
Autosomes: 10,202,908
X chromosome: 410,435
Autosomes: 76,768,387
X chromosome: 2,898,518
Processed data type
Alignment
Variant calls
Dataset ID of processed data
JGAD000690
JGAD000758 (joint call)
Processing method
List of processed data (Whole Genome Sequencing Analysis)
Data use policy
NBDC data sharing policy (JGAP000001)

WGS reference panel (autosomes + X)

Materials and participants
- WGS data (JGAD000220) of the biobank Japan project (N=1,037)
- WGS data of 1KGP p3v5 ALL (N=2,504) (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/)
  • Subject count
    1037 (Individual)
  • Cohort
    1000 Genomes Project, BioBank Japan
Experimental method
WGS
Target
N/A
Reference genome
GRCh37
Mapping
BWA-MEM (version 0.7.5a)
Read deduplication
picard (versions 1.106)
Realignment and base quality recalibration
GATK (ver.3.2-2)
Mapping quality
MAPQ < 20 were excluded (HaplotypeCaller)
QC and filtering
We set exclusion criteria for genotypes as follows:
(1) DP < 5, (2) GQ < 20, or (3) DP > 60 and GQ < 95, and regarded these genotypes as missing.
Variants with call rates < 90% were excluded before variant quality score recalibration (VQSR).
After VQSR, we excluded variants located in low-complexity regions (LCR), as defined by mdust software were excluded.
Finally, we used BEAGLE to impute missing genotypes.
Analysis method
GATK HaplotypeCaller (version 3.2-2)
Coverage (depth)
30x (aimed at depth)
Variant count
61,608,817 variants
Autosomes: 59,387,070 variants
X chromosome: 2,221,747 variants
Processed data type
Reference panel
Variant calls
Dataset ID of processed data
JGAD000679
Processing method
List of processed data (Imputation reference)
Data use policy
NBDC data sharing policy (JGAP000001)

WGS imputation panel (autosomes + X)

Materials and participants
[JGAD000867]
- WGS data (JGAD000220) of the biobank Japan project (N=1,026)
[JGAD000868]
- WGS data (JGAD000495) of the biobank Japan project (N=1,964)
  • Subject count
    2990 (Individual)
  • Cohort
    BioBank Japan
Experimental method
WGS
Target
N/A
Reference genome
GRCh38
Mapping
bwa mem (version 0.7.15)
Read deduplication
GATK MarkDuplicates (version 4.1.0.0)
Realignment and base quality recalibration
N/A
Mapping quality
N/A
QC and filtering
Germline whole genome sequencing data were processed, and the aggregate VCF was calculated. Variants were then filtered based on the following conditions:
(1) Variants that did not pass the VQSR filter were excluded
(2) Multi-allelic sites were excluded
(3) Variants with a call rate below 95% were excluded
(4) Variants deviating from Hardy-Weinberg equilibrium (P < 1e-10) were excluded
(5) Variants with a minor allele count (MAC) less than 2 were excluded
Analysis method
GATK HaplotypeCaller -ERC GVCF (version 4.1.0.0)
The ploidy for variant call was set as follows:
Autosomes and pseudoautosomal regions (PARs): ploidy=2
Non-PARs on the X chromosome: ploidy=2 (female) and ploidy=1 (male)
Non-PARs on the Y chromosome: ploidy=1 (male)
Processed data type
Reference panel
Variant calls
Dataset ID of processed data
JGAD000867
JGAD000868
Processing method
List of processed data (Imputation reference)
Data use policy
NBDC data sharing policy (JGAP000001)