Open steven-solar opened 1 year ago
Hi @steven-solar,
Absolutely, it's planned. The next version with updated annotations shall integrate the T2T-CHM13 build. Sorry for the delay,
Best, Véronique
hi @lgmgeo, just wondering if you have a sense of roughly when the CHM13 build might be implemented? Would love to use it on a current project.
Cheers, Georgie
Hi Georgie,
Really sorry because new ideas/features to investigate in AnnotSV are piling up... and currently I can't achieve everything (not to mention that I don't work full time on AnnotSV).
I'm not able to give you a precise date for this update. I apologize for the inconvenience.
Thank you for your interest in AnnotSV, Best, Véronique
No problem at all @lgmgeo, I understand. Thanks for letting me know :)
Looking forward to using AnnotSV with CHM13 when its ready, its a great tool!
Thank you for your understanding and kindness!
Just wondering how is going on with CHM13-T2T?
Sorry, I haven't started yet. But I always have it in mind.
@lgmgeo Thank you for this useful tool. I think it would be more widely used if it provided a way to create new references by user.
Any user interested in implementing new annotations/features in AnnotSV is welcome ;o) Please do not hesitate to fork the code and open a pull request.
The most time-consuming thing for me would be:
As most of the annotation files are not available in T2T-CHM13, this is really an obstacle to providing you this build in AnnotSV.
Here is the (incomplete) list of the GRCh38 files needed to be available in T2T-CHM13:
The most important (files must be downloaded in T2T-CHM13):
Others (liftover from GRCh38 to T2T-CHM13):
If anyone can help me to find the ones available in CHM13-T2T (at least the most important), that would be great.
Is it possible to use CHM13 as a reference for AnnotSV? Even if current annotations are just lifted from GRCh38 to CHM13 it would be very useful. Thank you!