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Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
©2017, Korean Society of Epidemiology
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Variant type | Allele frequency (%) | Genetic data format | No. per genome |
---|---|---|---|
Common | ≥5.0 | GWAS; resequencing; WES; WGS | 3-4 million |
Low frequency | 0.1-5.0 | GWAS; resequencing; exome array; WES; WGS | Various by ancestry background |
Private | <0.1 | WES; WGS | Differ by individual |
Sequencing source | Reads mapping | Variant calling | Haplotyping | Genotype imputation | |
---|---|---|---|---|---|
Sweden | Internal | BWA-Mem | GATK-HC | In progress | In progress |
Finland | External | BWA | GATK-UG | Completed | Completed |
United Kingdom | Internal + external | BWA | Samtools; bcftools | Completed | Completed |
Iceland | Internal | BWA | GATK-UG | Completed | Completed |
Japan | Internal | BWA-Mem | GATK-UG; bcftools | Completed | Completed |
Netherlands | External | BWA | GATK-UG | Completed | Completed |
GWAS, genome-wide association study; WES, whole exome sequencing; WGS, whole genome sequencing.
BWA, Burrows-Wheeler Aligner; GATK, Genome Analysis Toolkit; HC, haplotypecaller; UG, unified genotyper.