get sequence on reference genome of STR

[CocoMlle]

Hi !

I was wondering, do you think there is a simple way to get the sequence on reference genome of each STR detected by EHDN ? In order to build a vcf file.
Thanks a lot for your help,

Kind regards,
Marine

[egor-dolzhenko]

Hi Marine,

Thank you for the question. Someone in our team is working towards adding this functionality to the future versions of the program. Also, one of our collaborators created a script to annotate reference coordinates of expanded repeats detected by EHdn. If you'd like, I can reach out to them and ask if they would be willing to share their script?

Best wishes,
Egor

[CocoMlle]

Hi Egor,

It would be reallly nice of you yes, thanks a lot ! :)

Marine

[egor-dolzhenko]

Hi Marine,

Great! The script is here: https://github.com/francesca-lucas/ehdn-to-eh. I believe this script is work in progress and it might be useful to reach out to @francesca-lucas, the author of the script, about using it.

@francesca-lucas Francesca, would you recommend using the script as is? Or would it be better to wait?

Best wishes,
Egor