Different number of line in the bedMethyl table among samples

[HeleneMeMartin]

Hello,

I process 6 different samples that I mapped against the same reference genome (the mitochondria) using Dorado. Using Samtool coverage, I checked that all my sample covered 100% of my genome with with a minimum depth of 1. I then used modkit to generate a bedMethyl table and it turns out that my 6 samples have different number of rows.
Using modkit, I used the option --filter-threshold.

Does bedMethyl table output only site that have at least 1 called higher than the threshold ?
So that there is no lines like
Nmod = 0
Ncanonical = 0
Nother mod = 0
Nvalid_cov = 0
Nfail = 15

Thank you !

[ArtRand]

Hello @HeleneMeMartin

Does bedMethyl table output only site that have at least 1 called higher than the threshold ?
So that there is no lines like
Nmod = 0
Ncanonical = 0
Nother mod = 0
Nvalid_cov = 0
Nfail = 15

That's correct, as mentioned in the documentation, rows with Nvalid_cov = 0 are not reported. If you have a use case where this is a problem I could add a flag in the next release that outputs positions where all of the modification calls fall below the pass threshold.