Defining and cataloging variants in pangenome graphs

Structural variation causes some human haplotypes to align poorly with the linear reference genome, and this leads to "reference bias." A pangenome reference graph could ameliorate this bias by relating a sample to multiple reference assemblies. However, this approach requires a new definition of a "genetic variant." We define pangenome variants against a reference tree that includes all nodes (sequences) of the pangenome graph but only a subset of its edges; non-reference edges are variant edges. Analyzing the Minigraph-Cactus draft human pangenome reference graph, we identified 29.6 million genetic variants. 3.5 million variants (11.7%) have a reference allele that is not on GRCh38; these variants are difficult to detect without a pangenome reference and are found within tangled, multiallelic regions. We analyze the HLA-A and RHD gene regions and identify thousands of small variants entangled with several structural variants. We release the open-source pantree and a variant call format (VCF) variant catalog.