Sinan Shi
@sinanshi.bsky.social
You are right! Thank you for pointing it out. Running without the .bgi works. We should update the .bgi files soon!
February 5, 2024 at 10:45 PM
You are right! Thank you for pointing it out. Running without the .bgi works. We should update the .bgi files soon!
Sorry for the delay. I’ve been struggling with my UKB account. Will look at it tomorrow if it lets me.
February 1, 2024 at 10:23 PM
Sorry for the delay. I’ve been struggling with my UKB account. Will look at it tomorrow if it lets me.
I'll run regenie on Swiss army knife later today and come back to you to see if this works.
January 29, 2024 at 10:38 AM
I'll run regenie on Swiss army knife later today and come back to you to see if this works.
So firstly, --chr has to be an integer. This might be why the BGEN error. Could you try to leave out the --chr flag and run it again? I normally run without the --chr.
January 27, 2024 at 7:16 PM
So firstly, --chr has to be an integer. This might be why the BGEN error. Could you try to leave out the --chr flag and run it again? I normally run without the --chr.
Can you show me the command you are using? It works fine on my side.
January 25, 2024 at 10:40 AM
Can you show me the command you are using? It works fine on my side.
Does this error message come from the step1 or step2? Potentially things can go wrong: 1) GEL-UKB is aligned to hg38 reference genome and the previous version is hg19. 2) The chromosome IDs in GEL-UKB is "chrX" instead of "X" in the previous version.
January 24, 2024 at 2:40 PM
Does this error message come from the step1 or step2? Potentially things can go wrong: 1) GEL-UKB is aligned to hg38 reference genome and the previous version is hg19. 2) The chromosome IDs in GEL-UKB is "chrX" instead of "X" in the previous version.