kirvolque / variant_caller

Variant calling is a fundamental task in bioinformatics that involves identifying variants in DNA sequences. A variant caller is a software tool or algorithm that is used to detect genetic variations in genomic data. Variant Caller is a project developed by students Polytechnic University.

Variant Caller

Variant calling is a fundamental task in bioinformatics that involves identifying differences or variants in DNA sequences between a reference genome and a sample genome. A variant caller is a software tool or algorithm that is used to detect and annotate genetic variations in genomic data.

Variant Caller is a project developed by Polytechnic University students. It is a command-line application written in Java that allows you to call variants from DNA sequencing data in VCF (Variant Call Format) files.

Usage

To use Variant Caller, you must have a VCF file with your sequencing data. The application will then analyze the data and output a list of variants with their corresponding genomic positions, reference bases, alternative bases, and quality scores.

Technologies Used

This project uses the following technologies:

• Java - The programming language used to write the application.
• Maven - The build tool used to manage dependencies and build the project.
• JUnit - The testing framework used to write and run tests.
• Picard - The library used to perform various operations on SAM/BAM/CRAM and VCF files in Java.
• HTSJDK - A Java library for high-throughput sequencing data analysis.

Development

To build and test the application, you can use the following commands:

$ mvn compile # compile the application
$ mvn test # run tests