\documentclass{article} \usepackage{amsmath} \usepackage{float} \usepackage{amscd} \usepackage[tableposition=top]{caption} \usepackage{ifthen} \usepackage[utf8]{inputenc} %\VignetteIndexEntry{Using CODEX} \begin{document} \SweaveOpts{concordance=TRUE} \title{WES.1KG.WUGSC vignette} \author{Yuchao Jiang \\ yuchaoj@wharton.upenn.edu} \maketitle The dataset consists of assembled .bam files of whole exome sequencing (WES) data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center (WUGSC) are included. The 401st-500th exons from chromosome 22 of each sample are pre-extracted, sorted, indexed, and saved as .bam files for illustration purposes. \begin{table}[h] \begin{tabular}{|l|l|l|l|} \hline \textbf{Sample ID} & \textbf{Bam name} & \textbf{Population} & \textbf{Gender} \\ \hline NA06994 & NA06994.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam & CEU & male \\ \hline NA10847 & NA10847.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam & CEU & female \\ \hline NA11840 & NA11840.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam & CEU & female \\ \hline NA12249 & NA12249.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam & CEU & female \\ \hline NA12716 & NA12716.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam & CEU & male \\ \hline NA12750 & NA12750.mapped.ILLUMINA.bwa.CEU.exome.20130415.bam & CEU & male \\ \hline NA12751 & NA12751.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam & CEU & female \\ \hline NA12760 & NA12760.mapped.ILLUMINA.bwa.CEU.exome.20120522.bam & CEU & male \\ \hline NA12761 & NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam & CEU & female \\ \hline NA12763 & NA12763.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam & CEU & female \\ \hline NA18966 & NA18966.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam & JPT & male \\ \hline NA18967 & NA18967.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam & JPT & male \\ \hline NA18968 & NA18968.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & female \\ \hline NA18969 & NA18969.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & female \\ \hline NA18970 & NA18970.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & male \\ \hline NA18971 & NA18971.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & male \\ \hline NA18972 & NA18972.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam & JPT & female \\ \hline NA18973 & NA18973.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam & JPT & female \\ \hline NA18974 & NA18974.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & male \\ \hline NA18975 & NA18975.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & female \\ \hline NA18976 & NA18976.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & female \\ \hline NA18981 & NA18981.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & female \\ \hline NA18987 & NA18987.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & female \\ \hline NA18990 & NA18990.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & male \\ \hline NA18991 & NA18991.mapped.ILLUMINA.bwa.JPT.exome.20120522.bam & JPT & female \\ \hline NA19098 & NA19098.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & male \\ \hline NA19119 & NA19119.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & male \\ \hline NA19131 & NA19131.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & female \\ \hline NA19137 & NA19137.mapped.ILLUMINA.bwa.YRI.exome.20130415.bam & YRI & female \\ \hline NA19138 & NA19138.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & male \\ \hline NA19141 & NA19141.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & male \\ \hline NA19143 & NA19143.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & female \\ \hline NA19144 & NA19144.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & male \\ \hline NA19152 & NA19152.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & female \\ \hline NA19153 & NA19153.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & male \\ \hline NA19159 & NA19159.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & female \\ \hline NA19160 & NA19160.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & male \\ \hline NA19171 & NA19171.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & male \\ \hline NA19200 & NA19200.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & male \\ \hline NA19201 & NA19201.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & female \\ \hline NA19204 & NA19204.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & female \\ \hline NA19206 & NA19206.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & female \\ \hline NA19207 & NA19207.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & male \\ \hline NA19209 & NA19209.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & female \\ \hline NA19210 & NA19210.mapped.ILLUMINA.bwa.YRI.exome.20121211.bam & YRI & male \\ \hline NA19223 & NA19223.mapped.ILLUMINA.bwa.YRI.exome.20120522.bam & YRI & male \\ \hline \end{tabular} \end{table} \begin{thebibliography}{10} \providecommand{\url}[1]{[#1]} \providecommand{\urlprefix}{} \bibitem{1000-Genomes} Genomes Project, C., Abecasis, G.R., Altshuler, D., Auton, A., Brooks, L.D., Durbin, R.M., Gibbs, R.A., Hurles, M.E. and McVean, G.A.: \textbf{{A map of human genome variation from population-scale sequencing}} \emph{Nature} 2010, \textbf{467}:1061--1073. \end{thebibliography} \end{document}