Low number of interspersed duplications?

[GuillaumeHolley]

Hi,

I have recently aligned the CHM13 v1.0 assembly from the T2T consortium to the reference genome GRCh38.p13. I subsequently tried to detect SVs from the CHM13 alignment by using the following svim-asm command:

svim-asm haploid --max-sv-size 1000000 --sample CHM13 --reference_gap_tolerance 1000 --reference_overlap_tolerance 1000 --query_gap_tolerance 2000 --query_overlap_tolerance 2000 ./svim_chm13 chm13.bam hg38_p13.fa

This command results in only 4 interspersed duplications which seems quite low to me given the completeness of CHM13. I am also a little bit confused by these duplications: when I look at these 4 duplications, the first 3 of them are ending at the same location on GRCh38.p13 but they have very different lengths (all of them are PASS). Does it mean these are 3 different duplications occurring at different places in CHM13 or is it the same duplication but svim-asm cannot tell which of the 3 duplication lengths is the correct one?

Thank you for the help and the great software!

Guillaume

[GuillaumeHolley]

I ended up posting in the wrong repository (svim instead of svim-asm...). I am closing this one and opening a new issue in the correct repo.