LD between chromosome

[clairemerot]

Hi,
Is it posssible to calculate LD between chromosomes ( they are not actual chromosomes, they are scaffolds which might be physically linked)? I have not been able to find the proper option.

Alternative question: do you think it would be possible to calculate LD for Whole-genome set of SNPs (about 1 000 000)? Or is it unrealistic and I'd rather draw a subset by scaffold?
I'm interested in getting a matrix of LD for subsequent analysis with LDna for instance.

Thanks a lot for this promising new tool,
Claire

[corbinq]

Hi Claire,
Thanks for your question! Interchromosomal LD isn't currently supported, but it wouldn't be difficult to enable. I'd be happy to send an update once we've added that option

I haven't tried estimating LD genome-wide -- for only 1M SNPs, I would imagine that it's feasible (by default, LD is only estimated within sliding 1 Mbp windows)

Feel free to contact me with any suggestions or feedback

Thanks,
Corbin

[clairemerot]

Thanks for the fast reply. Yes, I'd be very interested when this is implemented, I'll be following your updates.
We are looking for rearrangements (inversions, fusions, etc), and LD can be very informative at a wide scale.
Also, you are probably aware of programs like LDna, https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12369, which allows looking for pattern in genome-wide LD (but requires the matrix of Ld to be calculated before!)

Thanks a lot,
Claire