Therefore, we created a PBSV and minigraph consensus to obtain consensus rare SVs. When used Phrank to rank the consensus rare SVs, we uncovered a deletion in KMT2E, which is likely to be a causal variant for a previously undiagnosed case.

We found that minigraph calls 29,964 in the twins, of which 84.96% are in both twins. PBSV calls 23,516 SVs in the same twins, of which 83.12% are in both twins.

Overall, we have found 204,551 SV alleles that are unique to the GA4K cohort, with the most common allele occurring in only 88 of the 574 haplotypes. This highlights the importance of personal de novo assemblies in finding rare SVs.

The additional sequence is mostly composed of simple repeats, satellites, and TEs. However, we estimate that at least 4.7 Mbp is unique sequence that is not repeats and is not present in HPRC or in the reference genome.

First, we assembled 574 rare disease haplotypes using HiFi, hifiasm and parental data. We validated these assemblies with Flagger developed within HPRC. Then we built a pangenome graph with minigraph on top of HPRC. This added 426 Mbps that is specific to the GA4K cohort.

Eh, Francis Fukuyama wrote worse