SNPlocs.Hsapiens.dbSNP.20120608

SNP locations for Homo sapiens (dbSNP Build 137)

Bioconductor version: Release (2.14)

SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 137. The source data files used for this package were created by NCBI on June 7-8, 2012, and contain SNPs mapped to reference genome GRCh37.p5. WARNING: Note that the GRCh37.p5 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).

Author: Herve Pages

Maintainer: H. Pages <hpages at fhcrc.org>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP.20120608")

Citation (from within R, enter citation("SNPlocs.Hsapiens.dbSNP.20120608")):

Documentation

PDF   Reference Manual

Details

biocViews AnnotationData, Genetics, Homo_sapiens
Version 0.99.9
License Artistic-2.0
Depends R (>= 2.10), IRanges, GenomicRanges, BSgenome(>= 1.25.6)
Imports methods, utils, IRanges, GenomicRanges, BSgenome
Suggests Biostrings, BSgenome.Hsapiens.UCSC.hg19(>= 1.3.19)
System Requirements
URL
Depends On Me ggtut
Imports Me
Suggests Me AllelicImbalance, cheung2010, GGtools, VariantFiltering

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