easyfinemap

A flexible framework for GWAS fine-mapping

• Documentation: https://Jianhua-Wang.github.io/easyfinemap
• GitHub: https://github.com/Jianhua-Wang/easyfinemap
• PyPI: https://pypi.org/project/easyfinemap/
• License: MIT

Features

• Formatting of summary statistics using smunger.
• Fast extraction of summary statistics for fine-mapping using tabix/bgzip.
• Checking and formatting of LD reference.
• Representation of variants using Unique SNP ID.
• Support for identifying independent loci using three methods: distance, LD clumping, and conditional analysis.
• Fine-mapping without the need for LD reference.
• Support for four LD-based fine-mapping tools and function-based fine-mapping.
• Fine-mapping combined with conditional analysis.