News: New Bioconductor package for dbSNP151
gravatar for Hervé Pagès
16 months ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Hi all,

A new SNPlocs package is now available with the content of dbSNP build 151:

SNPlocs packages contain SNP locations and alleles for various dbSNP builds. SNPs can be looked up by chromosome, range, or rs id, using snpsBySeqname()snpsByOverlaps(), or snpsById(), respectively.

SNPlocs.Hsapiens.dbSNP151.GRCh38 contains 596,534,862 single-base substitutions (i.e. SNPs of class snp). See ?SNPlocs.Hsapiens.dbSNP151.GRCh38 for how the SNPs in the package were curated. For comparison, the SNPlocs package for dbSNP build 150 (SNPlocs.Hsapiens.dbSNP150.GRCh38) contains 305,513,252 single-base substitutions.

The XtraSNPlocs packages contain the SNP locations and alleles for all the other classes of SNPs: in-del, heterozygous, microsatellite, etc...

BSgenome::available.SNPs() gives the list of all available SNPlocs and XtraSNPlocs packages:

> library(BSgenome)
> available.SNPs()
 [1] "SNPlocs.Hsapiens.dbSNP.20101109"     
 [2] "SNPlocs.Hsapiens.dbSNP.20120608"     
 [3] "SNPlocs.Hsapiens.dbSNP141.GRCh38"    
 [4] "SNPlocs.Hsapiens.dbSNP142.GRCh37"    
 [5] "SNPlocs.Hsapiens.dbSNP144.GRCh37"    
 [6] "SNPlocs.Hsapiens.dbSNP144.GRCh38"    
 [7] "SNPlocs.Hsapiens.dbSNP149.GRCh38"    
 [8] "SNPlocs.Hsapiens.dbSNP150.GRCh38"    
 [9] "SNPlocs.Hsapiens.dbSNP151.GRCh38"    
[10] "XtraSNPlocs.Hsapiens.dbSNP141.GRCh38"
[11] "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37"
[12] "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38"


ADD COMMENTlink modified 16 months ago • written 16 months ago by Hervé Pagès ♦♦ 14k
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