Pileup Option "--modified-bases" failed with "5hmC"

[Yang990-sys]

Hello,

It seems that the "--modified-bases" option has failed in the 5hmC analysis. Below is my script:

while 5mc and 6mA is normal :

[Yang990-sys]

I tested its performance on RNA modifications and found that it works normally for modifications on bases other than A and C, but disordered phenomena are still observed on A and C. The first column is the type of modification entered in "--modified-bases", the second column is the corresponding base, and the third column is the result in the bed file:

[ArtRand]

Hello @Yang990-sys

Thank you for noticing this bug and bringing it to my attention! I've attached a build where it's fixed. You can also use the released v0.6.0 Modkit with the flag --use-dynamic (a hidden flag) to get the correct behavior.

modkit_v0.6.1_8ec9da8.zip

[Yang990-sys]

Thank you very much. At the same time, I would like to know what content the hidden flags include. Could you update the way to learn about them in the documentation or the next version?

[Yang990-sys]

Hello , @ArtRand . With your script, Another bug has appeared where the fraction value exceeds 100 at some loci.

[ArtRand]

Hello @Yang990-sys, Could you try v0.6.1 and use the --high-depth flag? Documentation for that is here.