The SNPlocs.Hsapiens.dbSNP142.GRCh37 package

Description

This package contains SNP locations and alleles for Homo sapiens extracted from dbSNP Build 142.

Details

SNPs from dbSNP were filtered to keep only those satisfying the 3 following criteria:

• The SNP is a single-base substitution i.e. its type is "snp". Other types used by dbSNP are: "in-del", "mixed", "microsatellite", "named-locus", "multinucleotide-polymorphism", etc... All those SNPs were dropped.

• The SNP is marked as notwithdrawn.

• A single location on the reference genome (GRCh37.p5) is reported for the SNP, and this location is on chromosomes 1-22, X, Y, or MT.

SNPlocs packages always store the alleles corresponding to the plus strand, whatever the strand reported by dbSNP is (which is achieved by storing the complement of the alleles reported by dbSNP for SNPs located on the minus strand). In other words, in a SNPlocs package, all the SNPs are considered to be on the plus strand and everything is reported with respect to that strand.

Note

The source data files used for this package were created by the dbSNP Development Team at NCBI on October 14, 2014.

WARNING: The SNPs in this package are mapped to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a patched version of GRCh37 but the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct location but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

See http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html for more information about the GRCh37.p13 assembly.

See http://www.ncbi.nlm.nih.gov/snp, the SNP Home at NCBI, for more information about dbSNP.

See ?injectSNPs in the BSgenome software package for more information about the SNP injection mechanism.

See http://genome.ucsc.edu/cgi-bin/hgGateway?clade=mammal&org=Human&db=hg19 for more information about the Human Feb. 2009 (GRCh37/hg19) assembly used by the UCSC Genome Browser.

Author(s)

H. Pages

References

Human genome at NCBI with details about the GRCh37.p13 assembly: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html

SNP Home at NCBI: http://www.ncbi.nlm.nih.gov/snp

dbSNP Build 142 announcements: http://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2014q4/000147.html About the Human Feb. 2009 (GRCh37/hg19) assembly used by the UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgGateway?clade=mammal&org=Human&db=hg19

See Also

• getSNPlocs for how to access the data stored in this package.

• injectSNPs in the BSgenome package for more information about SNP injection.

• The VariantAnnotation software package to annotate variants with respect to location and amino acid coding.

Results