Base modification calls can be removed if they are low confidence based on the predicted modification probabilities.
In general, modkit will estimate a pass confidence threshold value based on the input data.
Threshold values for modifications on a primary sequence base can be specified on the command line with the --filter-threshold option.
For example to set a threshold for cytosine modifications at 0.8 and adenine modifications at 0.9 provide --filter-threshold C:0.8 --filter-threshold A:0.9.
Pass threshold values per base modification can also be specified.
For example, to specify a threshold for canonical adenine at 0.8 and 6mA at 0.9 use --filter-threshold A:0.8 --mod-thresholds a:0.9.
Or to specify a threshold of 0.8 for 5mC, 0.9 for 5hmC, and 0.85 for canonical cytosine: --filter-threshold C:0.85 --mod-thresholds m:0.8 --mod-thresholds h:0.9
Keep in mind that the --mod-threshold option will treat A, C, G, and T and "any-mod" as per the specification.