simmons_genome_diversity_oct_2016.Rnw

   1 \documentclass[ignorenonframetext]{beamer}
   2 \usepackage{fontspec}
   3 \setmainfont{FreeSerif}
   4 \setsansfont{FreeSans}
   5 \setmonofont{FreeMono}
   6 \usepackage{url}
   7 \usepackage{fancyhdr}
   8 \usepackage{graphicx}
   9 \usepackage[bf]{caption}
  10 \usepackage{rotating}
  11 \usepackage{wrapfig}
  12 \usepackage{fancybox}
  13 \usepackage{booktabs}
  14 % \usepackage{multirow}
  15 \usepackage{acronym}
  16 \usepackage{qrcode}
  17 \usepackage[backend=biber,natbib=true,hyperref=true,style=nature]{biblatex}
  18 \addbibresource{references.bib}
  19 % \usepackage[nomargin,inline,draft]{fixme}
  20 % \newcommand{\DLA}[1]{\textcolor{red}{\fxnote{DLA: #1}}}
  21 % \usepackage[hyperfigures,bookmarks,colorlinks,citecolor=black,filecolor=black,linkcolor=black,urlcolor=black]{hyperref}
  22 \usepackage{texshade}
  23 \usepackage{tikz}
  24 \usepackage{nameref}
  25 \usepackage{zref-xr,zref-user}
  26 \renewcommand*{\bibfont}{\tiny}
  27
  28 % The textpos package is necessary to position textblocks at arbitary
  29 % places on the page.  Use showboxes option to show outlines of textboxes.
  30 % \usepackage[absolute]{textpos}
  31 \usepackage[absolute,overlay]{textpos}
  32 \usepackage{mathtools,cancel}
  33
  34 \renewcommand{\CancelColor}{\color{red}} %change cancel color to red
  35
  36 \usepackage{multirow}
  37 \usepackage{array}
  38
  39 \usepackage{minted}
  40 \usepackage{tcolorbox}
  41 \usepackage{etoolbox}
  42 \BeforeBeginEnvironment{minted}{\begin{tcolorbox}}%
  43 \AfterEndEnvironment{minted}{\end{tcolorbox}}%
  44
  45 \mode<presentation>{
  46   \usetheme{CambridgeUS}
  47   \usecolortheme{crane}
  48   % http://identitystandards.illinois.edu/graphicstandardsmanual/generalguidelines/colors.html
  49   \definecolor{ilboldblue}{HTML}{002058}
  50   \definecolor{ilboldorange}{HTML}{E87722}
  51   \definecolor{ilblue}{HTML}{606EB2}
  52   \definecolor{ilorange}{HTML}{D45D00}
  53   \logo{\begin{tikzpicture}% Pale figure
  54       {\node[opacity=0.1]{\IfFileExists{figures/uofi_mark.pdf}{\includegraphics[width=2cm,height=1cm,keepaspectratio]{figures/uofi_mark}}{}%
  55         };}%
  56     \end{tikzpicture}}
  57 }
  58
  59 % remove navigation symbols
  60 \setbeamertemplate{navigation symbols}{}
  61
  62 \title[Ancestry]{Simmons Genome Diversity}
  63 \author[Don Armstrong]{Don L. Armstrong}
  64 \institute[IGB]{Institute for Genomic Biology, Computing Genomes
  65   for Reproductive Health, University of Illinois, Urbana-Champaign}
  66
  67 \begin{document}
  68
  69 <<load.libraries,echo=FALSE,results="hide",warning=FALSE,message=FALSE,error=FALSE,cache=FALSE>>=
  70 opts_chunk$set(dev="cairo_pdf",out.width="\\textwidth",out.height="0.8\\textheight",out.extra="keepaspectratio")
  71 #opts_chunk$set(cache=TRUE, autodep=TRUE)
  72 options(device = function(file, width = 8, height = 7, ...) {
  73   cairo_pdf(tempfile(), width = width, height = height, ...)
  74 })
  75 options(digits=2)
  76 library("data.table")
  77 library("ggplot2")
  78 library("reshape2")
  79 library("grid")
  80 library("xtable")
  81
  82 @
  83
  84 \IfFileExists{figures/relevant_xkcd.png}{\frame[plain]{\centering \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{figures/relevant_xkcd.png}
  85
  86     \url{https://xkcd.com/1706/}}}
  87
  88 \frame[plain]{\titlepage
  89   \begin{center}
  90     Code and slides are here:
  91
  92     \qrcode[padding]{http://dla2.us/p/genomdiv2016}
  93
  94     \url{http://dla2.us/p/genomdiv2016}
  95    \end{center}
  96 }
  97
  98
  99 \frame[plain]{
 100    \begin{center}
 101      \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/title.png}
 102    \end{center}
 103 }
 104
 105 \begin{frame}{Sampling}
 106   \begin{itemize}
 107   \item 142 populations from Africa, America, Oceania, South Asia,
 108     East Asia, and West Eurasia (mostly indigenous)
 109   \item 300 samples sequenced at 34-83 fold coverage by Illumina
 110   \item Aligned using BWA-MEM
 111   \item Genotyped using special version of GATK and Fermikit
 112   \item Data available in EBI ($n=279$, PRJEB9586) and dbGAP ($n=21$, ?)
 113   \end{itemize}
 114 \end{frame}
 115
 116
 117 \begin{frame}[fragile]{Alignment Pipeline}
 118   \begin{itemize}
 119   \item Aligned to the “decoy” version of the human reference
 120     (hs37d5); supposedly improves alignment in misassembled regions or
 121     regions with CNVs?
 122   \item PCR-free data, though they marked optical duplicates marked
 123     using samblaster
 124   \end{itemize}
 125 \begin{minted}{bash}
 126 ./htscmd bamshuf -Oun128 in.bam tmp-pre \
 127 | ./htscmd bam2fq -as aln-se.fq.gz - \
 128 | ./trimadap \
 129 | ./bwa mem -pt8 hs37d5.fa - \
 130 | ./samblaster \
 131 | samtools view -uS - \
 132 | samtools sort -@4 -m512M - out-pre
 133 \end{minted}
 134 \end{frame}
 135
 136 \begin{frame}[fragile]{Genotyping}
 137   \begin{itemize}
 138   \item Reference-bias; novel variants, GATK assumes reference is more
 139     likely which may not be the case. Use prior of
 140     $(0.4995,0.001,0.4995)$ instead of default
 141     $(0.9985,0.001,0.0005)$.
 142     \begin{itemize}
 143     \item Unclear what the effect of this change is on the calling
 144     \item Maybe worth thinking about?
 145     \end{itemize}
 146   \item Also used Fermikit; apparently has comparable call rates to
 147     GATK and platypus
 148   \end{itemize}
 149 \begin{minted}{bash}
 150   java -Xmx2g -jar GenomeAnalysisTK.jar \
 151   -T UnifiedGenotyper -I srt.aln.bam \
 152   -L CHR_ID -R hs37d5.fa -dcov 600 -glm SNP \
 153   -out_mode EMIT_ALL_SITES -stand_call_conf 5.0 \
 154   -stand_emit_conf 5.0 -inputPrior 0.0010 \
 155   -inputPrior 0.4995 -D dbsnp_138.b37.vcf \
 156   -o CHR_ID.vcf -A GCContent -A BaseCounts
 157 \end{minted}
 158 \end{frame}
 159
 160 \begin{frame}{Fermikit vs Platypus vs GATK}
 161   \begin{columns}
 162     \column{0.5\textwidth}
 163     \includegraphics[width=\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/supplemental-014.png}
 164     \column{0.5\textwidth}
 165   FermiKit and Platypus call 3.17M more sites than GATK, but unclear
 166   whether those are real sites or not; they go into this in much more
 167   detail than I've digested yet.
 168 \end{columns}
 169 \end{frame}
 170
 171 \begin{frame}{Relatedness of Populations}
 172   \begin{columns}
 173     \column{0.7\textwidth}
 174     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1a_1.png}
 175     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig1a_2.png}
 176     \column{0.3\textwidth}
 177     \begin{itemize}
 178     \item Neighbor joining tree based on pairwise divergence per nucleotide
 179     \item Deepest splits are in African populations
 180     \end{itemize}
 181   \end{columns}
 182 \end{frame}
 183
 184 \begin{frame}{PCA and Relatedness}
 185   \begin{center}
 186     \includegraphics[width=\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig_ed4.png}
 187   \end{center}
 188   \begin{itemize}
 189   \item Greatest variation seen in the African populations (orange)
 190   \item Other populations are much more similar to eachother in
 191     general
 192   \item Hapmap likely under-measured variation in Africa
 193   \end{itemize}
 194 \end{frame}
 195
 196 \begin{frame}
 197   \begin{center}
 198     \includegraphics[width=\textwidth,height=0.6\textheight,keepaspectratio]{genome_diversity_paper/fig1b.png}
 199   \end{center}
 200   \begin{itemize}
 201   \item Pygmy populations have lower X heterozygosity than other African populations
 202   \item Seen even after removing the third of X which is subject to selection
 203   \item Suggests that it's driven by demographic history, and the
 204     reduced diversity is due to male-driven admixture (also in non-Africans)
 205   \end{itemize}
 206 \end{frame}
 207
 208 \begin{frame}{Neanderthal Ancestry}
 209   \begin{center}
 210     \includegraphics[width=\textwidth,height=0.6\textheight,keepaspectratio]{genome_diversity_paper/fig1c.png}
 211   \end{center}
 212   \begin{itemize}
 213   \item No populations studied have a higher Neanderthal ancestry than
 214     East Asians
 215   \end{itemize}
 216 \end{frame}
 217
 218 \begin{frame}{Denisovan Ancestry}
 219   \begin{center}
 220     \includegraphics[width=\textwidth,height=0.6\textheight,keepaspectratio]{genome_diversity_paper/fig1d.png}
 221   \end{center}
 222   \begin{itemize}
 223   \item Oceanian groups have as much as 5\% Denisovan ancestry
 224   \item Eurasian differences in ancestry; some South Asians may have
 225     higher Denisovan than other Eurasians
 226   \end{itemize}
 227 \end{frame}
 228 g
 229
 230 \begin{frame}{Variation missed by hapmap}
 231   \begin{center}
 232     \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig_ed1.png}
 233   \end{center}
 234   \begin{itemize}
 235   \item Hapmap is missing up to 8\% of the heterozygous sites in parts
 236     of Africa
 237   \end{itemize}
 238 \end{frame}
 239
 240 \begin{frame}{Cross-coalescence rate}
 241   \begin{center}
 242     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2a.png}
 243     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2b.png}
 244   \end{center}
 245 \end{frame}
 246
 247 \begin{frame}{Cross-coalescence rate}
 248   \begin{center}
 249     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2c.png}
 250     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2d.png}
 251   \end{center}
 252 \end{frame}
 253
 254 \begin{frame}{Effective Population Size}
 255   \begin{center}
 256     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2e.png}
 257     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2f.png}
 258   \end{center}
 259 \end{frame}
 260
 261 \begin{frame}{Best-fitting admixture Graph}
 262   \begin{center}
 263     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig3.png}
 264   \end{center}
 265 \end{frame}
 266
 267
 268 \section*{References}
 269
 270 \begin{frame}[plain]{References}
 271   \begin{center}
 272     \mbox{}\vspace{-\baselineskip}
 273     \printbibliography[heading=none]
 274   \end{center}
 275 \end{frame}
 276
 277 \end{document}