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-\title[Ancestry]{Simmons Genome Diversity}
-\author[Don Armstrong]{Don L. Armstrong}
-\institute[IGB]{Institute for Genomic Biology, Computing Genomes
- for Reproductive Health, University of Illinois, Urbana-Champaign}
-
-\begin{document}
-
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-library("data.table")
-library("ggplot2")
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-
-@
-
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-
-\frame[plain]{\titlepage
- \begin{center}
- Code and slides are here:
-
- \qrcode[padding]{http://dla2.us/p/genomdiv2016}
-
- \url{http://dla2.us/p/genomdiv2016}
- \end{center}
-}
-
-
-\frame[plain]{
- \begin{center}
- \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/title.png}
- \end{center}
-}
-
-\begin{frame}{Sampling}
- \begin{itemize}
- \item 142 populations from Africa, America, Oceania, South Asia,
- East Asia, and West Eurasia (mostly indigenous)
- \item 300 samples sequenced at 34-83 fold coverage by Illumina
- \item Aligned using BWA-MEM
- \item Genotyped using special version of GATK and Fermikit
- \item Data available in EBI ($n=279$, PRJEB9586) and dbGAP ($n=21$, ?)
- \end{itemize}
-\end{frame}
-
-
-\begin{frame}[fragile]{Alignment Pipeline}
- \begin{itemize}
- \item Aligned to the “decoy” version of the human reference
- (hs37d5); supposedly improves alignment in misassembled regions or
- regions with CNVs?
- \item PCR-free data, though they marked optical duplicates marked
- using samblaster
- \end{itemize}
-\begin{minted}{bash}
-./htscmd bamshuf -Oun128 in.bam tmp-pre \
-| ./htscmd bam2fq -as aln-se.fq.gz - \
-| ./trimadap \
-| ./bwa mem -pt8 hs37d5.fa - \
-| ./samblaster \
-| samtools view -uS - \
-| samtools sort -@4 -m512M - out-pre
-\end{minted}
-\end{frame}
-
-\begin{frame}[fragile]{Genotyping}
- \begin{itemize}
- \item Reference-bias; novel variants, GATK assumes reference is more
- likely which may not be the case. Use prior of
- $(0.4995,0.001,0.4995)$ instead of default
- $(0.9985,0.001,0.0005)$.
- \begin{itemize}
- \item Unclear what the effect of this change is on the calling
- \item Maybe worth thinking about?
- \end{itemize}
- \item Also used Fermikit; apparently has comparable call rates to
- GATK and platypus
- \end{itemize}
-\begin{minted}{bash}
- java -Xmx2g -jar GenomeAnalysisTK.jar \
- -T UnifiedGenotyper -I srt.aln.bam \
- -L CHR_ID -R hs37d5.fa -dcov 600 -glm SNP \
- -out_mode EMIT_ALL_SITES -stand_call_conf 5.0 \
- -stand_emit_conf 5.0 -inputPrior 0.0010 \
- -inputPrior 0.4995 -D dbsnp_138.b37.vcf \
- -o CHR_ID.vcf -A GCContent -A BaseCounts
-\end{minted}
-\end{frame}
-
-\begin{frame}{Fermikit vs Platypus vs GATK}
- \begin{columns}
- \column{0.5\textwidth}
- \includegraphics[width=\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/supplemental-014.png}
- \column{0.5\textwidth}
- FermiKit and Platypus call 3.17M more sites than GATK, but unclear
- whether those are real sites or not; they go into this in much more
- detail than I've digested yet.
-\end{columns}
-\end{frame}
-
-\begin{frame}{Relatedness of Populations}
- \begin{columns}
- \column{0.7\textwidth}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1a_1.png}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1a_2.png}
- \column{0.3\textwidth}
- \begin{itemize}
- \item Neighbor joining tree based on pairwise divergence per nucleotide
- \item Deepest splits are in African populations
- \end{itemize}
- \end{columns}
-\end{frame}
-
-\begin{frame}{PCA and Relatedness}
- \begin{center}
- \includegraphics[width=\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig_ed4.png}
- \end{center}
- \begin{itemize}
- \item Greatest variation seen in the African populations (orange)
- \item Other populations are much more similar to eachother in
- general
- \item Hapmap likely under-measured variation in Africa
- \end{itemize}
-\end{frame}
-
-\begin{frame}
- \begin{center}
- \includegraphics[width=\textwidth,height=0.6\textheight,keepaspectratio]{genome_diversity_paper/fig1b.png}
- \end{center}
- \begin{itemize}
- \item Pygmy populations have lower X heterozygosity than other African populations
- \item Seen even after removing the third of X which is subject to selection
- \item Suggests that it's driven by demographic history, and the
- reduced diversity is due to male-driven admixture (also in non-Africans)
- \end{itemize}
-\end{frame}
-
-\begin{frame}{Neanderthal Ancestry}
- \begin{center}
- \includegraphics[width=\textwidth,height=0.6\textheight,keepaspectratio]{genome_diversity_paper/fig1c.png}
- \end{center}
- \begin{itemize}
- \item No populations studied have a higher Neanderthal ancestry than
- East Asians
- \end{itemize}
-\end{frame}
-
-\begin{frame}{Denisovan Ancestry}
- \begin{center}
- \includegraphics[width=\textwidth,height=0.6\textheight,keepaspectratio]{genome_diversity_paper/fig1d.png}
- \end{center}
- \begin{itemize}
- \item Oceanian groups have as much as 5\% Denisovan ancestry
- \item Eurasian differences in ancestry; some South Asians may have
- higher Denisovan than other Eurasians
- \end{itemize}
-\end{frame}
-g
-
-\begin{frame}{Variation missed by hapmap}
- \begin{center}
- \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig_ed1.png}
- \end{center}
- \begin{itemize}
- \item Hapmap is missing up to 8\% of the heterozygous sites in parts
- of Africa
- \end{itemize}
-\end{frame}
-
-\begin{frame}{Cross-coalescence rate}
- \begin{center}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2a.png}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2b.png}
- \end{center}
-\end{frame}
-
-\begin{frame}{Cross-coalescence rate}
- \begin{center}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2c.png}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2d.png}
- \end{center}
-\end{frame}
-
-\begin{frame}{Effective Population Size}
- \begin{center}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2e.png}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2f.png}
- \end{center}
-\end{frame}
-
-\begin{frame}{Best-fitting admixture Graph}
- \begin{center}
- \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig3.png}
- \end{center}
-\end{frame}
-
-
-\section*{References}
-
-\begin{frame}[plain]{References}
- \begin{center}
- \mbox{}\vspace{-\baselineskip}
- \printbibliography[heading=none]
- \end{center}
-\end{frame}
-
-\end{document}