Question about gap deletions, gap ins and gap dups

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Official home of genome aligner based upon notion of Cactus graphs

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Question about gap deletions, gap ins and gap dups #1520

Open lsoler-clavel opened 1 week ago

lsoler-clavel commented 1 week ago

Hello, I've been working on a five-species elasmobranch alignment and am not sure what the difference between deletions/gap deletions is (same for insertions and GI, duplications etc) when extracting the bed coordinates from the hal output. Could you help me understand?

Thank you in advance!

glennhickey commented 3 days ago

Hi, you are not alone with these questions. See https://github.com/ComparativeGenomicsToolkit/hal/issues/308

I think we need updated tooling for this, and I'm hoping to get something implemented to that end in the coming months. In the meantime I suggest you consider using the MAF format to double check the mutations where possible.