Pileup in v6 not giving correct methylation versus the versions before

[ArnavBharti]

I have bam files which were obtained when I ran modified basecalling using guppy for 5mC, and 5hmC. I ran pileup in version 5, and it gave modifications for both m and h. When I ran the new pileup command, I am only getting modifications for m and not h. I have attached a comparison of the outputs below. In the new pileup command, I have specified 5mC and 5hmC in --modified-bases.

/ * old */
Pv_Sal1_chr01	2376	2377	h	2	-	2376	2377	255,0,0	2 50.00 1 0 1 0 0 0 6
Pv_Sal1_chr01	2376	2377	m	2	-	2376	2377	255,0,0	2 50.00 1 0 1 0 0 0 6

/* new */
Pv_Sal1_chr01	2376	2377	h	1	-	2376	2377	255,0,0	1	0.00	0	0	1	0	1	0	6
Pv_Sal1_chr01	2376	2377	m	1	-	2376	2377	255,0,0	1	100.00	1	0	0	0	1	0	6

Help would be appreciated @ArtRand. I can provide any other details if required. This workflow's other commands are mentioned in #580

[ArtRand]

Hello @ArnavBharti,

Looks like one of the calls is being tabulated in N_fail with v0.6.1. Is it possible that the filter threshold is every so slightly different and it's causing one of the calls to fail? If you have the logs I can take a look. If you can attach or email a small subset of the bam I can take a look. Email is art.rand[at]nanoporetech[dot]com.