First release of nf-core/phaseimpute available

By Louis Le Nézet
bioinformatics imputation nf-core

First release of nf-core/phaseimpute

I’m excited to announce the first official release of the nf-core/phaseimpute pipeline, developed in collaboration with Anabella Trigila and the amazing nf-core community. This pipeline is designed to streamline the genetic imputation process, specifically focusing on the preparation of haplotype reference panels for imputing genomic data of target individuals.

While the initial version of the pipeline is focused on low-pass sequencing data, it supports state-of-the-art imputation tools such as Glimpse, Stitch and Quilt. In the future, we plan to expand support for SNP chip array data with tools like impute5, Beagle5, and Minimac4.

How it works

The nf-core/phaseimpute pipeline simplifies and automates several critical steps involved in genetic imputation. Here’s an overview of how the pipeline operates:

phaseimpute_metromap

1) Reference panel pre-processing. The first step involves processing your reference panel, ensuring that it’s compatible with the selected imputation tools. This includes operations like normalization, phasing, and extraction of relevant sites.

2) Imputation of target data. Next, the pipeline uses the selected software (Glimpse, Stitch, or Quilt) to impute your target BAM or VCF files, filling in missing genetic data based on the reference panel.

3) Simulation of target files. You can also simulate target files with varying sequencing depths, enabling you to test how different depths impact imputation accuracy.

4) Imputation accuracy evaluation. The pipeline allows you to compare the imputed data against a truth set. This truth set can be either computed using bcftools mpileup or provided as a VCF file of known genotypes.

Key Features

  • Easy integration with popular imputation tools (Glimpse, Stitch, Quilt, and future support for impute5, Beagle5, Minimac4).
  • Comprehensive imputation workflow, from reference panel preparation to target data imputation.
  • Simulated depth testing to evaluate the impact of sequencing depth on imputation accuracy.
  • Comparison with truth sets to validate imputed data against known genotypes.

Acknowledgments

This pipeline was built using the powerful nf-core v3.0.2 framework and Nextflow v24.10.1. We leveraged the excellent nf-schema plugin for parameter validation, ensuring that the pipeline is both flexible and robust. Additionally, all modules, subworkflows, and workflows were rigorously tested using nf-test.

More information

Feel free to explore the first release of the pipeline here, and stay tuned for future updates as we continue to enhance its capabilities!