SNP and indel variant concordance. Venn diagrams illustrating the concordance of SNPs and indels called by DeepVariant from a representative subsample of HG005 Chr 6 reads aligned by Moni-align, vg map, and vg giraffe to the pan-MHC Chr 6 pangenome. The top row shows the concordance of GIAB HG005 MHC variants present in the pangenome, restricted to the high-confidence MHC regions, identified by DeepVariant. The bottom row shows the concordance of the full set of GIAB HG005 MHC variants, similarly restricted to high-confidence MHC regions, identified by DeepVariant. The number at the bottom right of each diagram indicates the number of variants that were not identified by any of the three aligners.
