GT field

[kdelmore]

Hi - Thanks for developing this tool.

Just wondering if there's a way to get genotypes. We are comparing alignments of several individuals to our reference and would like to get an idea how the SVs look at the population scale (e.g., combining vcfs with jasmine and conducting some population genetic analyses). If not I guess we just have to use the data as presence absence (i.e., no 0/1).

Thanks, Kira

[mnshgl0110]

Hi Kira,

Currently, syri cannot genotype SVs as it is still not possible to accurately compare/merge large structural rearrangements between multiple genomes. We are developing new strategies to do this, however, there is nothing concrete yet.

Best
Manish

[nainai77]

Hi - Thanks for developing this tool.

Just wondering if there's a way to get genotypes. We are comparing alignments of several individuals to our reference and would like to get an idea how the SVs look at the population scale (e.g., combining vcfs with jasmine and conducting some population genetic analyses). If not I guess we just have to use the data as presence absence (i.e., no 0/1).

Thanks, Kira

Hi,

I am curious to know if you have attempted any genotyping of the SVs, or if there were other endeavors undertaken subsequent to this. I am interested in performing genotype analysis on the outcomes related to structural variations.

Best
Ayn

[mnshgl0110]

Hi Ayn,
We have a new tool in development that identifies all syntenic regions in multiple genomes (https://github.com/schneebergerlab/msyd). Currently, it does not call SVs directly, but it is fair to consider all non-syntenic regions as SVs. I am not sure whether this would fit your requirements properly, but other than msyd I do not know of other tools aiming to solve the challenge of multi-genome structural comparisons.