## Forward-Only PBWT (Positional Burrows-Wheeler Transform)

## Introduction
The Forward-Only PBWT is an efficient method to find blocks of matches. The Positional Burrows-Wheeler Transform (PBWT) was developed by Richard Durbin as a representation of haplotype data for storing the data and finding matches efficiently among a set of haplotypes. The input data for Forward-Only PBWT is phased genotype data (in VCF format) and a genetic map.

## Dependencies
- C++ (at least GCC 5)  
- GNU Make  
- GNU getopt
- Bash  

## Installation
To install the program clone the repository to a local folder using:

`git clone https://github.com/ZhiGroup/bi-PBWT.git`

Enter the repository folder and compile the program:

`cd "bi-PBWT/Forward-Only PBWT"`  
`make`

## Usage Instructions
Type  
`./run.sh`  
by itself to show the help page.  

|         Option         |                         Parameter                        |                                                    Description                                                    |
|:----------------------:|:--------------------------------------------------------:|:-----------------------------------------------------------------------------------------------------------------:|
| `-r` or `--readVcf`    | Full or relative file path to input VCF file             | Sets the input VCF file on which to run PBWT.                                                                     |
| `-m` or `--map`    	 | Full or relative file path to Genetic Mapping file       | Sets the Genetic Mapping file.                                                                                    |
| `-o` or `--writeTo`    | Full or relative file path and filename for output files | Sets the location and filename for PBWT output files. The default option is the VCF filename.                     |
| `-l` or `--length`     | Block length (in units of centimorgan (cM))              | Sets the minimum length requirement for blocks. The default value is 1 centimorgan.                               |
| `-w` or `--width`      | Block width                                              | Sets the minimum number of haplotypes required for a block to be reported. The default value is 100 haplotypes.   |

An example:  
`./run.sh --readVcf "example.vcf" --map "example.rmap" --writeTo "output" --length 0.1 --width 500` 

## Genetic Mapping Format
The format of the genetic mapping file must be 2 space-separated fields per line: "site number" "genetic mapping".

## Results
When finished executing, PBWT will generate 1 file with the extensions ".blocks".

The file ".blocks" represents each block on its own line with five space-separated fields `<starting genomic location of block> <ending genomic location of block> <starting genetic location of block> <ending genetic location of block> <width of block>` followed by space seperated ID's of all the haplotypes in the block. IDs are suffixed with either "-0" or "-1" indicating the first and second haplotype of the individual ID, respectively.