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---
title: "SNP analysis"
author: "Daniel Cook"
date: "March 4, 2015"
output: 
  html_document:
    toc: true
    theme: cosmo
---

```{r SETUP}
output <- opts_knit$get("rmarkdown.pandoc.to")
opts_chunk$set(warning=F, message=F, echo=F, dev="pdf")
opts_chunk$set(cache.path="cache/mt")
opts_chunk$set(fig.path="figures/mt/")
output <- "html"
if (output=="html") opts_chunk$set(fig.width=11, fig.height=11)
if (output=="docx") opts_chunk$set(fig.width=6,  fig.height=6)
```