README.Rmd

---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

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MIPanalyzer
------------

`MIPanalyzer` is a tool for analyzing MIP (molecular inversion probe) data. It performs the following functions:

- Reading in raw data, usually in the form of a `vcf` file produced by [MIPwrangler](https://github.com/bailey-lab/MIPWrangler)
- Filtering samples and loci based on coverage, missingness, and other metrics
- Performing simple population genetic analyses, such as PCA and basic pairwise distance metrics

All documentation, including installation instructions and tutorials, are on [the MIPanalyzer website](https://mrc-ide.github.io/MIPanalyzer).


Version History
------------

The current release version of the software is v1.1.0, released 12 Dec 2023.


Contributors
------------
- [Bob Verity](https://github.com/bobverity)
- [OJ Watson](https://github.com/ojwatson)
- [Nick Brazeau](https://github.com/nickbrazeau)