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Hi Sayathan, thanks a lot for your answer, it is very clear! Indeed, mainly for rare variants I couldn't replicate the Rsq values I see in the imputation output VCFs....

Dear Yang, Thank you very much for explanation! I made a quick test on the same sample with this command: `regtools junctions extract -a 8 -m 50 -M 500000 $bamfile...

Hi again, I now have completed rerunning the sQTL mapping pipeline for regtools-quantified data, and compared it with the old data (that was quantified with old Leafcutter pipeline [bam2junc.sh]). I...

Dear Yang, Sorry for the delayed response, it has been a rather strange period of time! Indeed, I agree that the main step to be investigated should be the number...

Dear Yang, For a comprehensive comparison between the old and the new pipeline where you can also easily use the same files for further comparison/testing, I used the example GEUVADIS...

Dear Yang @goldenflaw (and other contributors), I made a new analysis; because, as I indicated in the above comment, I think the example test bam files provided in this repository...

Thank you for developing annotaTR for addressing this issue @gymreklab! I have been making some tests this week, here is my experience (also for the future reference for others who...

Thanks a lot @gymreklab! To go through the comments and the questions: 1) `annotaTR --version` gives me also `6.0.2`. I cloned the master repository of TRTools last Monday (August 26),...

Hi, I also wanted to ask this question - whether there are any plans soon to implement binary phenotypes for associaTR. It would be a really great addition to associaTR!...

Thanks a lot @gymreklab! I have actually noticed earlier this week that my another issue #209 was marked as completed with the release of this new annotaTR tool, and since...