dbSNP

Overview

dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.

Publication

Sherry, S.T., Ward, M. and Sirotkin, K. (1999) dbSNP—Database for Single Nucleotide Polymorphisms and Other Classes of Minor Genetic Variation. Genome Res., 9, 677–679.

VCF File

Example

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	10177	rs367896724	A	AC	.	.	RS=367896724;RSPOS=10177;dbSNPBuildID=138; \ 
      SSR=0;SAO=0;VP=0x050000020005130026000200;GENEINFO=DDX11L1:100287102;WGT=1; \
      VC=DIV;R5;ASP;G5A;G5;KGPhase3;CAF=0.5747,0.4253;COMMON=1; \
      TOPMED=0.76728147298674821,0.23271852701325178

Parsing

From the VCF file, we're mainly interested in the following:

• rsID from the ID field
• CAF from the INFO field

Global allele extraction

The global major and minor alleles are extracted based on the frequency of the alleles provided in the CAF field. The global minor allele frequency is the second highest value of the CAF comma delimited field (ignoring '.' values).

Tie Breaking: Global Major Allele

If there are two candidates for global major and the reference allele is one of them, we prefer the reference allele.

Tie Breaking: Global Minor Allele

If there are two candidates for global minor and the reference allele is one of them, we prefer the other allele. If the reference allele is not involved, they are chosen arbitrarily.

Equal Allele Frequency Example (2 alleles)

chr1	100	A	C	CAF=0.5,0.5

We will select A to be the global major allele and C to be the global minor allele.

Equal Allele Frequency Example (3 alleles)

chr1	100	A	C,T	CAF=0.33,0.33,0.33

We will select A to be the global major allele and either C or T is chosen (arbitrarily) to be the global minor allele.

Equal Allele Frequency in Alternate Alleles

chr1	100	A	C,T	CAF=0.2,0.4,0.4

We will select C or T to be arbitrarily assigned to be the global major or global minor allele.

Equal Allele Frequency Between Reference & Alternate Allele

chr1	100	A	C,T	CAF=0.2,0.2,0.6

We will select T to be the global major allele and C to be the global minor allele.

Known Issues

Known Issues

If there are multiple entries with different CAF values for the same allele, we use the first CAF value.

Download URL

https://ftp.ncbi.nih.gov/snp/organisms/

JSON Output

"dbsnp":[
   "rs1042821"
]

Field	Type	Notes
dbsnp	string array	dbSNP rsIDs

Building the supplementary files

You can generate dbSNP supplementary annotation files by yourself. Please refer to SAUtils section for more details.