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Upscaling SV detection to a multi-population level.

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# SV-Pop

[![release](https://img.shields.io/github/v/release/mattravenhall/SV-Pop)](https://github.com/mattravenhall/SV-Pop/releases) [![docs](https://img.shields.io/badge/read%20the%20wiki-green)](https://github.com/mattravenhall/SV-Pop/wiki) [![doi](https://img.shields.io/badge/doi-10.1186/s12859--019--2718--4-yellow)](https://doi.org/10.1186/s12859-019-2718-4)

SV-Pop performs post-discovery SV analysis and visualisation; it contains two modules for these purposes. Both modules should work out of the box, but it's a good idea to run preflightchecks.py (in Analysis/) to check that all dependencies are installed, and to optionally add SVPop to your PATH.

Extended documentation, including specifics regarding input files, is present on this repo's [wiki](https://github.com/mattravenhall/SV-Pop/wiki).

## Analysis Module
<img src="https://raw.githubusercontent.com/mattravenhall/SV-Pop/master/Images/Preview_Analysis.png" alt="Preview Analysis" width="800"/>

### Quick start:
```bash
SVPop -h
```

### Functions
- `DEFAULT`: Process individual vcf files to population-level lists.
- `CONVERT`: Convert a variant output file into a window file.
- `FILTER`: Filter a variant output file by a range of factors.
- `MERGE-CHR`: Merge per-chromosome variants files into one file.
- `MERGE-MODEL`: Merge by-model variants files into one file.
- `SUBSET`: Create a subset of a given variant or window file.
- `STATS`: Produce summary statistics for a variant or window files.
- `PREPROCESS`: Process analysis output files for visualisation.

Expanded help can be found on the [wiki](https://github.com/mattravenhall/SV-Pop/wiki/Analysis-Expanded-Help).

## Visualisation Module
<img src="https://raw.githubusercontent.com/mattravenhall/SV-Pop/master/Images/Preview_Visualisation.png" alt="Preview Visualiser"/>

### Quick start:
```bash
SVPop --PREPROCESS --variantFile=YOUR_PREFIX
Rscript easyRun.r
```

### Expected Input
The visualisation module will expect the following files in Visualisation/Files/:
- `<model>_Variants.csv`: Reformatted variants file.
- `<model>_Windows.csv`: Reformatted windows file.
- `<model>_AllIndex.csv`: Locations of all variants, for faster indexing.
- `<model>_FrqIndex.csv`: Subset of AllIndex for 'frequent' (>5%) variants only.
- `annotation.txt`: The annotation file used for your SVPop Analysis run (in tsv format).

These files can be created from a default SVPop Analysis run with `SVPop --PREPROCESS --variantFile=YOUR_PREFIX`.

Expanded help can be found on the [wiki](https://github.com/mattravenhall/SV-Pop/wiki/Visualisation-Expanded-Help).

## Citation
Matt Ravenhall, Susana Campino and Taane G. Clark. *BMC Bioinformatics* 2019 **20**:136. https://doi.org/10.1186/s12859-019-2718-4

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