Canary

Canary converts MaCH mldose and mlinfo dosage files into PLINK1- and PLINK2-compatible formats to enable genome-wide association analyses of imputed genotype data.

Key Features:

• Automatic conversion: Automates transformation of MaCH mldose and mlinfo files into PLINK-compatible formats via a single command-line invocation.
• Singularity containerization: Encapsulates all software dependencies within Singularity containers to enable reproducible execution across HPC environments.
• Preinstalled GWAS software: Includes GWAS tools such as PLINK and Bioconductor inside the container for downstream analysis.
• Public dataset support: Supports conversion of MaCH-formatted imputed data commonly distributed by repositories such as dbGaP and the Women's Health Initiative (WHI).

Scientific Applications:

• GWAS with imputed dosages: Produces PLINK1/PLINK2-compatible files from MaCH dosage output to enable association testing using imputed genotype dosages.
• Re-analysis of public cohorts: Facilitates re-analysis of dbGaP and WHI datasets by converting their MaCH dosage files into formats accepted by standard GWAS workflows.
• Integration with analysis workflows: Enables downstream use of PLINK and Bioconductor-based pipelines on converted imputed datasets.

Methodology:

Conversion of MaCH mldose and mlinfo files into PLINK1/PLINK2-compatible formats is performed within Singularity containers that encapsulate PLINK, Bioconductor, and other necessary software dependencies.