Canary: an automated tool for the conversion of MaCH imputed dosage files to PLINK files.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35896971", "kind": "science-record", "revision": 3, "content_hash": "sha256:81760fcb73e0d31f7c11768757965bd8d7d55879d69049cacb84845aff61429a", "created_at": "2026-11-01T18:14:59Z", "updated_at": "2026-11-01T21:28:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Canary: an automated tool for the conversion of MaCH imputed dosage files to PLINK files.", "doi": "10.1186/s12859-022-04822-8", "pmid": "35896971", "authors": ["Adam N Bennett", "Jethro Rainford", "Xiaotai Huang", "Qian He", "Kei Hang Katie Chan"], "journal": "BMC bioinformatics", "year": 2022, "abstract": "BACKGROUND: Previous studies have demonstrated the value of re-analysing publicly available genetics data with recent analytical approaches. Publicly available datasets, such as the Women's Health Initiative (WHI) offered by the database of genotypes and phenotypes (dbGaP), provide a wealthy resource for researchers to perform multiple analyses, including Genome-Wide Association Studies. Often, the genetic information of individuals in these datasets are stored in imputed dosage files output by MaCH; mldose and mlinfo files. In order for researchers to perform GWAS studies with this data, they must first be converted to a file format compatible with their tool of choice e.g., PLINK. Currently, there is no published tool which easily converts the datasets provided in MACH dosage files into PLINK-ready files.\nRESULTS: Herein, we present Canary a singularity-based tool which converts MaCH dosage files into PLINK-compatible files with a single line of user input at the command line. Further, we provide a detailed tutorial on preparation of phenotype files. Moreover, Canary comes with preinstalled software often used during GWAS studies, to further increase the ease-of-use of HPC systems for researchers.\nCONCLUSIONS: Until now, conversion of imputed data in the form of MaCH mldose and mlinfo files needed to be completed manually. Canary uses singularity container technology to allow users to automatically convert these MaCH files into PLINK compatible files. Additionally, Canary provides researchers with a platform to conduct GWAS analysis more easily as it contains essential software needed for conducting GWAS studies, such as PLINK and Bioconductor. We hope that this tool will greatly increase the ease at which researchers can perform GWAS with imputed data, particularly on HPC environments.", "claims": [{"id": "claim-data-access", "statement": "Canary along with detailed instructions can be found at https://github.com/anb94/Canary. This tool is a singularity container and therefore requires singularity installed locally. The conversion tool is written in Shell. The dataset used as an example herein is the Women's Health Initiative Clinical Trial and Observational Study. The study data can be downloaded from the dbGaP web site, under phs000200.v12.p3 (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000200.v12.p3), if granted approval. The most recent version of Canary can be found on GitHub at https://github.com/anb94/Canary. The archived version referenced in the manuscript can be found on GitHub at https://github.com/anb94/Canary/tree/canary_archive.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35896971", "locator": "sections[16] \"Availability of data and materials\" paragraph 2", "quote": "Canary along with detailed instructions can be found at https://github.com/anb94/Canary. This tool is a singularity container and therefore requires singularity installed locally. The conversion tool is written in Shell. The dataset used as an example herein is the Women's Health Initiative Clinical Trial and Observational Study. The study data can be downloaded from the dbGaP web site, under phs000200.v12.p3 (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000200.v12.p3), if granted approval. The most recent version of Canary can be found on GitHub at https://github.com/anb94/Canary. The archived version referenced in the manuscript can be found on GitHub at https://github.com/anb94/Canary/tree/canary_archive."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35896971"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35896971", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12859-022-04822-8", "sha256": "sha256:aa250d77be4c720b5c7120af6ee5ffd101f4f55d2cae3b2ce6ddcbbb33797349", "bytes": 30388, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12859-022-04822-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9327220", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "genetic_association", "specific": "gwas", "label": "Genetic association (GWAS / linkage / MR)", "dsl_operations": ["gwas_locus_scan"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["genotype_phenotype_table"], "evidence": {"score": 0.7, "band": "medium", "quote": "Genome-Wide Association Studies"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["gwas_locus_scan"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: gwas."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["Canary along with detailed instructions can be found at https://github.com/anb94/Canary. This tool is a singularity container and therefore requires singularity installed locally. The conversion tool is written in Shell. The dataset used as an example herein is the Women's Health Initiative Clinical Trial and Observational Study. The study data can be downloaded from the dbGaP web site, under phs000200.v12.p3 (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000200.v12.p3), if granted approval. The most recent version of Canary can be found on GitHub at https://github.com/anb94/Canary. 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