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\name{writeVcf}
\alias{writeVcf}
\alias{writeVcf,VCF,character-method}
\alias{writeVcf,VCF,connection-method}
\title{Write VCF files}
\description{Write Variant Call Format (VCF) files to disk}
\usage{
\S4method{writeVcf}{VCF,character}(obj, filename, index = FALSE, ...)
\S4method{writeVcf}{VCF,connection}(obj, filename, index = FALSE, ...)
}
\arguments{
\item{obj}{Object containing data to be written out. At
present only accepts \linkS4class{VCF}.
}
\item{filename}{The character() name of the VCF file, or a connection
(e.g., \code{\link{file}()}), to be written out. A connection opened
with \code{open = "a"} will have header information written only if
the file does not already exist.}
\item{index}{Whether to bgzip the output file and generate a tabix index.
}
\item{\dots}{Additional arguments, passed to methods.
}
}
\details{A VCF file can be written out from data in a \code{VCF} file. More
general methods to write out from other objects may be added in the future.
\code{writeVcf} conforms to the VCF standards on the 1000 Genomes Project
web site (see references).
}
\value{VCF file
}
\references{
\url{http://vcftools.sourceforge.net/specs.html} outlines the VCF
specification.
\url{http://samtools.sourceforge.net/mpileup.shtml} contains
information on the portion of the specification implemented by
\code{bcftools}.
\url{http://samtools.sourceforge.net/} provides information on
\code{samtools}.
}
\author{Valerie Obenchain <vobencha@fhcrc.org> and Michael Lawrence}
\seealso{
\code{\link{readVcf}}
}
\examples{
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
out1.vcf <- tempfile()
out2.vcf <- tempfile()
in1 <- readVcf(fl, "hg19")
writeVcf(in1, out1.vcf)
in2 <- readVcf(out1.vcf, "hg19")
writeVcf(in2, out2.vcf)
in3 <- readVcf(out2.vcf, "hg19")
stopifnot(all(in2 == in3))
## write to console
writeVcf(in1, stdout())
## write incrementally
out3.vcf <- tempfile()
con <- file(out3.vcf, open="a")
writeVcf(in1[1:2,], con)
writeVcf(in1[-(1:2),], con)
close(con)
readVcf(out3.vcf, "hg19")
}
\keyword{manip}
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