% \VignetteIndexEntry{VariantTools Example Data}
% \VignetteKeywords{data, variants}
% \VignettePackage{VariantToolsData}
\documentclass[10pt]{article}

<<style-Sweave, eval=TRUE, echo=FALSE, results=tex>>=
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\bioctitle[VariantTools Data]{Data for the VariantTools Tutorial}

\author{Michael Lawrence\thanks{\email{michafla@gene.com}}\\Genentech}
\date{\today}

\begin{document}

\maketitle
\packageVersion{\Sexpr{BiocStyle::pkg_ver("VariantToolsData")}}
\tableofcontents
\newpage

\section{Overview}

In support of the tutorial vignette for the \Biocpkg{VariantTools}
package, \Biocpkg{VariantToolsData} provides a dataset derived from
sequencing a 50/50 mixture of the HapMap samples NA12878 and NA19240,
where the mixing was performed in triplicate (\cite{dataset}). The
data are subset over the region of TP53 (+/- 1 Mb).

There are several summarized objects accessible via \Rcode{data()} and
documented in the package manual. In addition, there are data files
stored here:
<<files>>=
dir(system.file("extdata", package="VariantToolsData"))
@ 
These include FASTQ files with the raw reads and BAM files with the
alignments, as well as a VCF file derived from dbSNP.

Please see the \Biocpkg{VariantTools} vignette to learn how to work
with these data with \Bioconductor{}.

\bibliography{intro}

\end{document}