Dynamic mu-PBWT

Dynamic mu-PBWT is a dynamic compressed PBWT. This tool supports dynamic updates (insertion/deletion) of the index in its compressed format and supports long match query.

Related paper: "Dynamic mu-PBWT: Dynamic Run-length Compressed PBWT for Biobank Scale Data"

Contact Author: Pramesh Shakya (pramesh.shakya@ucf.edu)

System Requirements

This tool has been tested on Linux environment.

GCC Compiler: >= g++11

Dependencies

DYNAMIC library by Nicola Prezza and Alan Kuhnle (https://github.com/xxsds/DYNAMIC)

Installation

Open a terminal and follow these steps:

1. Clone the github repository: git clone https://github.com/ucfcbb/Dynamic-mu-PBWT

2. cd into the cloned folder: cd ./Dynamic-mu-PBWT

3. Configure the build: ./configure

4. Build the project: ./build

There will be a build directory which contains the following executables dmupbwt, insert and delete.

Test the installation by running the executables as follows: ./build/dmupbwt, ./build/insert, and ./build/delete. It will print out the usage details for each of the executables.

Usage

Construction of Dynamic mu-PBWT and Long match query

To construct Dynamic mu-PBWT on the input vcf or run long match query algorithm. Following are the usage details when you run ./build/dmupbwt:

Flag	Description	Details
-i <file>	Path to reference VCF file (string)	uncompressed VCF file
-q <file>	Path to query VCF file (string)	uncompressed VCF file
-o <file>	Path to output match file (string)	matches(L-long matches or set maximal matches) between haplotypes of query panel and the reference panel
-L <value>	length threshold (sites) (int)	minimum length threshold for long match query
-c	call set maximal match (bool)	call set maximal matches between query panel and reference panel
-v	verbose (bool)	prints out memory usage and other information about the panel

Construction

To construct Dynamic mu-PBWT on the input vcf: ./build/dmupbwt -i ./test_data/ref.1.vcf -v

Long Match query

To find long match queries on Dynamic mu-PBWT with verbose output: ./build/dmupbwt -i ./test_data/ref.1.vcf -q ./test_data/query.1.vcf. -o ./test_data/out_matches -L 3 -v

Set Maximal Match query

To find set maximal match queries on Dynamic mu-PBWT with verbose output: ./build/dmupbwt -i ./test_data/ref.1.vcf -q ./test_data/query.1.vcf. -o ./test_data/out_matches -c -v

Insertion

To insert haplotypes on empty Dynamic mu-PBWT:

./build/insert -i ./test_data/ref.1.vcf -v

To insert haplotypes on non-empty Dynamic mu-PBWT:

./build/insert -i ./test_data/ref.1.vcf -q ./test_data/query.1.vcf -v

Deletion

To randomly delete all the haplotypes from a given Dynamic mu-PBWT:

./build/delete -i ./test_data/ref.1.vcf -v

This builds the Dynamic mu-PBWT on the input VCF file and randomly deletes all the haplotypes.