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user-friendly pipeline for GWAS fine-mapping.

Project description

easyfinemap

pypi python Build Status codecov License: MIT PyPI download month Build Status

A flexible framework for GWAS fine-mapping

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.

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