PRC: Support other reference genomes

[justinjj24]

Reviewers (David Bujold – McGill and Abeer Fadda – EGA bioinformatics QC lead) of Product Review Committee (PRC) suggest: Following our discussion, you should add to "https://ga4gh.github.io/quality-control-wgs/roadmap_v2/" the fact that other reference genomes will also be supported.

[justinjj24]

Intent to provide QC metrics covering definitions, implementations, and the resulting QC reporting schema that will also support alternative reference genome assemblies to GRCh38 (in particular GRCh37/hg19 for backward compatibity with readily processed WGS data collections)

[justinjj24]

Worgroup in its September 2025 meeting, agreed to support GRCh37/hg19 for backward compatibity

Here are some short, clear reasons why GRCh37/38 remain the primary reference genomes compared to T2T, pan-genome, or other assemblies:

Global adoption & standardization – GRCh37/38 are the most widely used references across research, clinical, and regulatory settings.

Well-curated & refined They have undergone years of refinement, annotation, and validation.

Extensive tool support Most pipelines, algorithms, and bioinformatics tools are built around GRCh37/38.

Rich database integration Key resources (dbSNP, ClinVar, gnomAD, 1000 Genomes, ENCODE, etc.) are aligned to GRCh37/38.

Regulatory & clinical standards Widely accepted for reporting variants in diagnostics and publications.

Backward compatibility Long history of use makes data sharing and comparison easier.

New assemblies like T2T or the human pan-genome are technically superior, but adoption is slower because the ecosystem is deeply anchored in GRCh37/38.