lgmgeo / AnnotSV

Annotation and Ranking of Structural Variation
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Using CHM13 as a reference #164

Open steven-solar opened 1 year ago

steven-solar commented 1 year ago

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!

lgmgeo commented 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

georgiesamaha commented 1 year ago

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

lgmgeo commented 1 year ago

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

georgiesamaha commented 1 year ago

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!

lgmgeo commented 1 year ago

Thank you for your understanding and kindness!

quanc1989 commented 7 months ago

Just wondering how is going on with CHM13-T2T?

lgmgeo commented 7 months ago

Sorry, I haven't started yet. But I always have it in mind.

quanc1989 commented 7 months ago

@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.

lgmgeo commented 7 months ago

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.

lgmgeo commented 7 months ago

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.