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 theID
fieldCAF
from theINFO
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 |