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\name{VariantAnnotation-defunct}
\alias{VariantAnnotation-defunct}
\alias{readVcfLongForm}
\alias{readVcfLongForm,TabixFile,character,GRanges-method}
\alias{readVcfLongForm,TabixFile,character,missing-method}
\alias{readVcfLongForm,TabixFile,character,RangedData-method}
\alias{readVcfLongForm,TabixFile,character,RangesList-method}
\alias{readVcfLongForm,TabixFile,character,ScanVcfParam-method}
\alias{readVcfLongForm,character,character,ScanVcfParam-method}
\alias{readVcfLongForm,character,character,missing-method}
\alias{readVcfLongForm,character,missing,missing-method}
\alias{dbSNPFilter}
\alias{regionFilter}
\alias{MatrixToSnpMatrix}
\title{Defunct Functions in Package \code{VariantAnnotation}}
\description{
The functions or variables listed here are no longer part
of \code{VariantAnnotation}.
}
\section{usage}{
## Defunct in 1.9.z
readVcfLongForm()
## Removed in 1.9.z
dbSNPFilter()
regionFilter()
MatrixToSnpMatrix(callMatrix, ref, alt, ...)
}
\details{
## Defunct in 1.9.z:
\code{readVcfLongForm} has been replaced by \code{expand}.
## Removed in 1.9.z:
\code{dbSNPFilter} and \code{regionFilter} have been replaced by
\code{filterVcf}.
\code{MatrixToSnpMatrix} has been replaced by \code{genotypeToSnpMatrix}.
}
\author{
Valerie Obenchain <vobencha@fhcrc.org>
}
\seealso{
\code{\link{filterVcf}}, \code{\link{genotypeToSnpMatrix}}.
}
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