\name{SNPlocs.Hsapiens.dbSNP.20110815}
\docType{package}

\alias{SNPlocs.Hsapiens.dbSNP.20110815-package}
\alias{SNPlocs.Hsapiens.dbSNP.20110815}

\alias{COMPATIBLE_BSGENOMES}


\title{The SNPlocs.Hsapiens.dbSNP.20110815 package}

\description{
  This package contains SNP locations and alleles for Homo sapiens
  extracted from dbSNP Build 134.
}

\details{
  SNPs from dbSNP were filtered to keep only those satisfying the 3
  following criteria:
  \itemize{
    \item 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.
    \item The SNP is marked as notwithdrawn.
    \item A single location on the reference genome (GRCh37.p2) is
          reported for the SNP.
  }
}

\note{
  The source data files used for this package were created by the dbSNP
  Development Team at NCBI on 15 August 2011.

  WARNING: The SNPs in this package are mapped to reference genome GRCh37.p2.
  Note that the GRCh37.p2 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 \url{http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html}
  for more information about the GRCh37.p2 assembly.

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

  See \code{?\link[BSgenome]{injectSNPs}} in the BSgenome software
  package for more information about the SNP injection mechanism.

  See \url{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.
}

\references{
  Human genome at NCBI with details about the GRCh37.p2 assembly:
  \url{http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/}
  \url{http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html}

  SNP Home at NCBI:
  \url{http://www.ncbi.nlm.nih.gov/snp}

  dbSNP Build 134 announcement:
  \url{http://www.ncbi.nlm.nih.gov/projects/SNP/docs/build134.txt}

  About the Human Feb. 2009 (GRCh37/hg19) assembly used by
  the UCSC Genome Browser:
  \url{http://genome.ucsc.edu/cgi-bin/hgGateway?clade=mammal&org=Human&db=hg19}
}

\author{H. Pages}

\seealso{
  \code{\link{getSNPlocs}} for how to access the data stored in this package.

  \code{\link[BSgenome]{injectSNPs}} in the BSgenome package for more
  information about SNP injection.
}

\keyword{package}