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Databases

The file formats in the static_data/db folder are mostly .vcf or .bed files. We provide the following databases:

Database Version Reference genome
COSMIC v72 GRCh37
dbNSFP 2.9 GRCh37/hg19
dbSNP b128 mm9
dbSNP b128 NCBIM37
dbSNP b142 GRCh37
dbSNP b144 GRCh38
dbSNP b147 GRCh37
dbSNP b147 GRCh38
dbSNP b150 GRCh37
dbSNP b150 GRCh38
DGV 2015-07-23 GRCh37
ExAC release0.3 GRCh37/hg19
ExAC release0.3.1 GRCh37/hg19
giab NA12878_HG001/NISTv2.19 GRCh37
goldenpath variable GRCh37
goldenpath variable hg19
goldenpath variable mm9
goldenpath variable NCBIM37
SangerMousegenomesProject REL-1211-SNPs_Indels mm9
SangerMousegenomesProject REL-1211-SNPs_Indels NCBIM37
UK10K cohort REL-2012-06-02 GRCh37

The directory structure is as follows:

static_data/db
├── COSMIC
│   └── v72
│       └── GRCh37
├── dbNSFP
│   └── 2.9
├── dbSNP
│   ├── b128
│   │   ├── mm9
│   │   └── NCBIM37
│   ├── b142
│   │   └── GRCh37
│   ├── b144
│   │   └── GRCh38
│   └── b147
│       ├── GRCh37
│       └── GRCh38
├── DGV
│   └── 2015-07-23
│       └── GRCh37
├── ExAC
│   ├── release0.3
│   └── release0.3.1
├── giab
│   └── NA12878_HG001
│       └── NISTv2.19
├── goldenpath
│   └── variable
│       ├── GRCh37
│       ├── hg19
│       ├── mm9
│       └── NCBIM37
├── SangerMouseGenomesProject
│   └── REL-1211-SNPs_Indels
│       ├── mm9
│       └── NCBIM37
└── UK10K_cohort
    └── REL-2012-06-02

Last update: January 6, 2022