AVVA SV call set for HC1-T and HC1-N

Contigs from each assembly were aligned to the N genome using MUMer (version 4, with parameters --mum -l 100 -c 500). The coordinates of the alignment blocks were sorted by query. AVVA (https://github.com/jeff-sc-chu/AVVA) was used to call inversions and translocations based on MUMer alignment blocks. Each SV found from HC1-T was evaluated to ensure it is cancer-specific such that 1) SV bordering assembly gaps were removed, 2) SV found in assembly-based HC1-N call set was removed, and 3) SV found in map-based HC1-N call set was removed.