I've been looking into haplotypecaller local assembly algorithm recently. I found out something after reading related documents. That is,
- It fails to assemble when there are tens of consecutively adjacent variants in an active region.
- It fails to assemble when an active region happens to be repeat-rich（regions like this will be skipped because it may cause cycles in graph）
Does anybody know why it fails to assemble and how we improve the assembler?
Thanks in advance,
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