How is the super large INV defined/formed ?

[jxlabWzZ]

hi, sir Thank you for providing an excellent SV detection software. However, I have problems with SV detection for large SVs, especially for >1Mb INV. Because i find that the alignment region in *.filtered.coords are very fragmented.

for example: syri identified a large inv : chrY 29220000 40054179 chrY 34889612 44124518 INV INV 10834179

*.filtered.coords:

[mnshgl0110]

I am not sure I understand what is the issue here, but I assume it is related to large gaps in inversions. I have recently added a parameter to control that https://github.com/schneebergerlab/syri/commit/f70300bc5913f18ac77b8da88df3e4d2518a7f5d . Maybe you can try this (by downloading and installing syri from GitHub).

If this is not what you were asking, then could you please provide more information about what is the issue.

[jxlabWzZ]

Thank you for your reply. I would like to ask why there is a MB-level of structural variation, while mummer only report SYN blocks of several hundred KB at most.

[mnshgl0110]

MUMmer (nucmer) reports alignments between genomes. The alignments can break if there is significant local sequence divergence. Syri tries to identify large rearrangements spanning these local sequence divergence and can therefore identify >MB long structural rearrangements.

[jxlabWzZ]

I got it, thank you very much.