lohhlamod

Introduction

lohhlamod is the original LOHHLA algorithm re-engineered in modern style that

• offers additional features/metrics for better interpretation
• offers runtime speedup
  • separates HLA realignment from LOH detection
  • maximizes vectorized operations whenever possible
  • uses data.table for efficient data processing
• provides better output layout and makes intermediate result per allele in RDS format accessible
• provides proper packaging for ease use in multi-user HPC environment
• removes hardcoded path presets for better code maintenance

Installation

It is recommended to use docker for building and running lohhlamod.

docker compose build --pull

Run LOH analysis

Please refer to the documentation for details.

Citation

Please cite the original HLALOH paper, its Bitbucket repository, and the lohhlamod repository.

License

• lohhlamod fully respects all LICENSE requirments imposed by the original LOHHLA tool.
• lohhlamod is free to use for all non-commercial parties.