Imputation Pipelines

Welcome to the Imputation project, a comprehensive suite of pipelines designed for phasing, imputation, meta-imputation, and post-imputation analysis. You can take full control of your genomics data, ensuring high-quality imputation and analysis.

Key Features

• Build Your Own Local Reference Panel: Utilize whole genome sequencing data to construct a personalized local reference panel.
• Impute Genotyping Array Data: Leverage your local reference panel to impute missing data from genotyping arrays.
• Meta-Imputation: Combine imputation results from multiple panels to optimize data quality and integrity.
• Post-Imputation Analysis: Evaluate and assess the performance of your imputation using post-imputation analysis scripts.

Pipelines Overview

1. Statistical Phasing Pipeline

Construct a high-quality reference panel. (statistical phasing)

2. Pre-Phasing and Imputation Pipeline

Prepare your data and perform imputation. (imputation, pre-phasing)

3. Meta-Imputation Pipeline

Combine results from multiple imputation panels. (meta-imputation)

4. Post-Imputation Analysis Pipelines

Assess and validate the performance of your imputation. (Imputed vs Truth, Imputed vs Imputed)

Getting Started

To get started, please refer to each pipeline's README.md file.

Support and Contact

Questions? Issues? Feel free to open an issue on our GitHub repository, or contact me directly at mohadese.sayahiandehkordi@mail.mcgill.ca. We welcome your feedback and are committed to providing support to ensure your success with our pipelines.

Author: Mohadese Sayahian Dehkordi