Long Inversions not detectable 2.19 to 2.24

[DHmeduni]

I tested 2.17 to 2.24 using an inversion between two large homologous domains. 2.17 and 2.18 detection was possible using structural variant callers. Everything after that was unable to be found. I'll help find the reason if I can, but I don't have the software skills to look under the hood too much. I'm guessing this has to do with the algorithm change in 2.19.

[lh3]

Do you have the sequence? Thanks

[DHmeduni]

I created a reference sequence with an inversion, then mapped normal gDNA nanopore sequences against it, works with 2.17 and 2.18 using npinv, but not with anything 2.19 or above. If you need the data, I can't supply you with the sequenced data, but with the reference incl. the inversion (several hundred MB) you could use NanoSim to create sequencing data based on the normal reference sequence or inverted reference sequence and then map to the opposite. I'd need a place to upload the inverted reference sequence if you would like. But since we are looking to publish this all, not sure my PI wants to give anything to a third party. I'll have to ask in the meantime. Best Regards, David

On Wed, 26 Apr 2023 at 00:27, Heng Li @.***> wrote:

Do you have the sequence? Thanks

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