Connection to third-party tools or platforms

About

The Connect module in KGGA enables integration with external tools and platforms for additional genetic analyses. It leverages KGGA’s robust capabilities for cleaning, annotating, and preprocessing large-scale genotype data. Processed data is stored in efficient formats —such as PLINK’s BED or PGEN binary files on disk —or maintained as optimized computing objects in RAM. These outputs serve as inputs for third-party tools or platforms, facilitating follow-up genetic analysis of complex traits or diseases.

Functions in the Connect Module

The Connect module currently supports four specialized functions, each seamlessly integrated with a specific tool or platform:

1. PLINK2: Generates genotypes and phenotypes in PLINK’s PGEN format after preprocessing, enabling direct analysis with PLINK2.
2. PLINK: Produces genotypes and phenotypes in PLINK’s BED format after preprocessing, supporting analysis with PLINK (version ≤ 1.9).
3. GCTA: Creates genotypes and phenotypes in PLINK’s BED format after preprocessing, allowing direct analysis with GCTA.
4. Python: Provides Java APIs to access computing objects in RAM, enabling users to perform custom analyses in Python. This option requires proficiency in both Java and Python programming.

Basic Usage

The following command demonstrates how to preprocess data and connect to a third-party tool:

java -jar kgga.jar <clean/annotate/prune> \
     --input <input1> \
     --input <input2> \
     --output <output> \
     [options] \
     --plink2/--plink/--gcta [tools' options]

Key Parameters

• : Specifies the preprocessing task (e.g., cleaning, annotating, or pruning genotype data).
• --input --input : Defines input files for preprocessing.
• --output
  : Sets the output file or directory for processed data.
• [options]: Additional parameters for preprocessing (specific to the task).
• --plink2/--plink/--gcta: Selects the third-party tool for analysis, generating compatible output formats and launching the tool directly.