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filtering.md

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Partitioning pass and fail base modification calls.

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.

Further details

  1. Examples of how thresholds affect base modification calls.
  2. Numerical details of how thresholds are calculated on the fly.