Commit 50b4d38c authored by Laros's avatar Laros
Browse files

Updated lecture.

parent 251f9e20
......@@ -2,7 +2,7 @@
\title{Variant Calling}
\providecommand{\myConference}{Hogeschool Leiden}
\providecommand{\myDate}{Friday, October 10, 2014}
\providecommand{\myDate}{Thursday, October 14, 2015}
\author{Jeroen F. J. Laros}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
......@@ -34,12 +34,12 @@
% First page of the presentation.
\section{Introduction}
\begin{frame}
\frametitle{Sequencers: HiSeq}
\frametitle{Sequencers: Illumina}
\begin{minipage}[t]{0.48\textwidth}
\begin{figure}
\includegraphics[width=\textwidth]{hiseq_2000}
\caption{HiSeq 2000.}
\caption{HiSeq 2500.}
\end{figure}
\end{minipage}
\hfill
......@@ -49,7 +49,7 @@
\item High throughput.
\item Paired end.
\item High accuracy.
\item Read length $2 \times 150$bp.
\item Read length $2 \times 125$bp.
\item Relatively long run time.
\item Relatively expensive.
\end{itemize}
......@@ -57,7 +57,7 @@
\end{frame}
\begin{frame}
\frametitle{Sequencers: Ion Torrent}
\frametitle{Sequencers: Life Technologies}
\begin{minipage}[t]{0.48\textwidth}
\begin{figure}
......@@ -80,7 +80,7 @@
\end{frame}
\begin{frame}
\frametitle{Sequencers: Ion Torrent}
\frametitle{Sequencers: Life Technologies}
\begin{minipage}[t]{0.48\textwidth}
\begin{figure}
......@@ -139,7 +139,7 @@
Not all aligners can deal with indels.
\begin{itemize}
\item Only a couple of years ago, only SNPs were considered.
\item Only a couple of years ago, only substitutions were considered.
\begin{itemize}
\item Bowtie.
\end{itemize}
......@@ -289,7 +289,7 @@
\end{frame}
\begin{frame}
\frametitle{False positive SNPs.}
\frametitle{False positive substitutions.}
Can occur because of misalignment near (large) deletions or insertions.
\bigskip
......@@ -301,7 +301,7 @@
What is often seen:
\begin{itemize}
\item A number of reads that indicate an indel.
\item Some reads that do not span the indel properly indicate SNPs.
\item Some reads that do not span the indel properly indicate substitutions.
\end{itemize}
\pause
......@@ -319,7 +319,7 @@
\includegraphics[trim=12cm 9cm 9cm 3.3cm, clip, height=\textheight]
{27bpDel}
\end{center}
\caption{False positive SNPs.}
\caption{False positive substitutions.}
\label{}
\end{figure}
\end{frame}
......@@ -327,7 +327,7 @@
\begin{frame}
\emph{Base Alignment Quality} (BAQ) realignment:
Remove SNPs around indels.
Remove substitutions around indels.
\begin{center}
\fbox{
......@@ -541,7 +541,7 @@
Create a VCF file with Bcftools (part of Samtools).
\bigskip
\begin{lstlisting}[language=none, caption=Call SNPs and indels with Samtools.]
\begin{lstlisting}[language=none, caption=Call substitutions and indels with Samtools.]
bcftools view -bvcg in.mpileup > out.bcf
bcftools view out.bcf > out.vcf
\end{lstlisting}
......@@ -568,7 +568,7 @@
Filter the results.
\bigskip
\begin{lstlisting}[language=none, caption=Call SNPs and indels with Samtools.]
\begin{lstlisting}[language=none, caption=Call substitutions and indels with Samtools.]
vcfutils.pl varFilter -d 8 -D 50 out.vcf > flt.vcf
\end{lstlisting}
......@@ -589,10 +589,10 @@
\begin{frame}[fragile]
\frametitle{VarScan}
SNP and indel calling with VarScan.
Substitution and indel calling with VarScan.
\bigskip
\begin{lstlisting}[language=none, caption=Call SNPs with VarScan.]
\begin{lstlisting}[language=none, caption=Call substitutions with VarScan.]
java -jar VarScan.jar mpileup2snp in.mpileup \
--output-vcf > out.vcf
\end{lstlisting}
......@@ -1059,30 +1059,6 @@
\end{figure}
\end{frame}
\begin{frame}
\frametitle{DVD}
The \emph{Diagnostic Variant Database}.
\begin{itemize}
\item Share variants found in exome sequencing experiments.
\item Find functionally relevant variants.
\end{itemize}
\bigskip
\pause
Technical details:
\begin{itemize}
\item Store coverage information to determine reference calls.
\item Disambiguation of variant descriptions.
\item Pooling without loss of information.
\item Duplicate sample detection.
\begin{itemize}
\item Allows for re-annotation without polluting the database.
\end{itemize}
\item Encrypted connection with authentication.
\end{itemize}
\end{frame}
\section{Pitfalls}
\begin{frame}
\frametitle{Things to remember}
......
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