GIAB Problematic Regions tracks for human (hg38 and hs1)

[Gerardo Perez]

Hello Everyone,

We are pleased to announce the release of the Genome in a Bottle (GIAB) Problematic Regions tracks for the hg38 and hs1 human assemblies. The tracks provide stratifications of the genome to evaluate variant calls in complex regions and it is designed for use with Global Alliance for Genomic Health (GA4GH) benchmarking tools like hap.py. It includes regions with low complexity, segmental duplications, functional regions, and difficult-to-sequence areas. The GIAB Problematic Regions composite track consists of four subtracks:

• All difficult regions – Genome In a Bottle: all difficult regions
• LowMap+SegDup – Genome In a Bottle: lowMap+SegDup regions
• Not difficult regions – Genome In a Bottle: not difficult regions
• Not lowMap+SegDup – Genome In a Bottle: not lowMap+SegDup mapping regions

We would like to thank the Genome in a Bottle Consortium, Telomere-to-Telomere Consortium, and NIST for providing this data. We would also like to thank Megna Chalamala, Jairo Navarro, and Gerardo Perez for the creation and release of these tracks.