Unverified Commit 59688e67 authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros
Browse files

Added presentation.

parent b36ccda6
\documentclass[slidestop]{beamer}
\author{Jeroen F.J. Laros}
\title{PGx project update}
\providecommand{\mySubTitle}{Work package 2}
\providecommand{\myConference}{}
\providecommand{\myDate}{22-08-2020}
\providecommand{\myGroup}{Bioinformatics}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\usetheme{lumc}
\setlength{\fboxsep}{0pt}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title slide.
\makeTitleSlide{\fbox{\includegraphics[height=3cm]{card}}}
% First page of the presentation.
\section{Introduction}
\makeTableOfContents
\section{Work package 2}
\subsection{Overview}
\begin{pframe}
PacBio Long Read Pipeline.
\begin{itemize}
\item Variant Calling pipeline for PacBio data.
\end{itemize}
\bigskip
Heterogeneous Data Exploration.
\begin{itemize}
\item Full inventory of available data types, the extent to which they can
be used and available techniques for enrichment of phasing data.
\end{itemize}
\end{pframe}
\begin{pframe}
Variant Disambiguation.
\begin{itemize}
\item Model for the disambiguation of (partially) phased variants.
\item Methods for working with overlapping variant descriptions.
\item Publication on variant disambiguation for the PGx domain.
\end{itemize}
\bigskip
Predictive Modelling.
\begin{itemize}
\item Genotype to phenotype model.
\item Proposal for AI based inference of phenotype.
\item Publication on genotype to phenotype modelling.
\end{itemize}
\end{pframe}
\section{Status update}
\subsection{Finished activities}
\begin{pframe}
Pipeline.
\begin{itemize}
\item Raw PacBio data to per sample VCF files using GATK4.
\item Runs on our new HPC cluster.
\item Container technology for improved stability.
\item Extensive regression testing.
\end{itemize}
\vfill
\permfoot{\url{https://gatk.broadinstitute.org/hc/en-us}}
\end{pframe}
\subsection{Ongoing activities}
\begin{pframe}
Other variant callers.
\begin{itemize}
\item Longshot.
\item DeepVariant.
\end{itemize}
\bigskip
Validation.
\begin{itemize}
\item First tests with version 3.3 of the GIAB truth set.
\item Now looking at a recently released truth set that was made using
PacBio and linked-read data.
\item Different variant callers and filtering options.
\end{itemize}
\vfill
\permfoot{\url{https://github.com/pjedge/longshot}}
\permfoot{\url{https://github.com/google/deepvariant}}
\permfoot{\url{https://www.biorxiv.org/content/10.1101/2020.07.24.212712v1}}
\end{pframe}
\subsection{Next steps}
\begin{pframe}
Phasing.
\begin{itemize}
\item Read backed phasing using WhatsHap.
\end{itemize}
\bigskip
At a later stage, we will add phasing by descent.
\bigskip
In an other project (Mutalyzer), we have developed a theoretical basis for
variant disambiguation.
\begin{itemize}
\item Investigate to which extent this can be used in the PGx project.
\item Make an implementation for PGx (publication).
\end{itemize}
\vfill
\permfoot{\url{https://whatshap.readthedocs.io/en/latest/}}
\end{pframe}
% Make the acknowledgements slide.
\makeAcknowledgementsSlide{
\begin{tabular}{ll}
\bf Human Genetics & \bf KFT \\
R.R. van den Berg & M. van der Lee \\
S.L. Kloet & J.J. Swen \\
R. Menafra & H.J. Guchelaar \\
M.A. Santcroos & \\
J.K. Vis & \\
S.M. van der Maarel & \\
\end{tabular}
}
\end{document}
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../../submodules/presentation/beamerthemelumc.sty
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