modkit pileup --interval-size 1000000 --chunk-size 100

[blipinskiaima]

Hello

When running modkit pileup on the same BAM and reference genome, I observed output differences depending on whether interval and chunk parameters were set.

Commands

modkit pileup <input.bam> <output_default.bedMethyl>
modkit pileup --interval-size 1000000 --chunk-size 100 <input.bam> <output_chunked.bedMethyl>

Data

• Same sample (129.4M reads)
• Same basecalling, alignment, and input BAM
• Same modkit version and compute environment

Results
bedMethyl lines by default = 2,397,050
bedMethyl lines by with --interval-size 1000000 --chunk-size 100 = 2,397,256
Difference: +206 lines

Even with identical inputs, enabling --interval-size and --chunk-size produces a slightly larger bedMethyl output. This suggests these parameters may affect determinism or completeness in CpG methylation calls.
Could the team please confirm if this behavior is expected, or if it should be flagged for further investigation in a future release?

We stay in touch.
Many thanks in advance.
Best,
Boris

[ArtRand]

Hello @blipinskiaima,

I've sent you email with this same message, but for folks reading this issue board I'll report the salient points here.

One thing to check first is that the estimated pass threshold value is the same between runs that you are comparing. This value is output to the console and to the log file specified with --log. There is a new version of pileup coming very soon which has a completely re-worked mechanism. If you'd be willing to test this, since you're taking a hard look at your data, I would appreciate early feedback.