-p signal to noise ratio

[blex-max]

It's not made explicit which way round the input signal to noise ratio is interpreted - I assume for example that the default 0.33 means noise 1:3 signal for a base to be called. Since it's not documented, could you clarify for me? Thanks very much.

[tobiasrausch]

It's a peak ratio. Let's call the maximum trace signal at a given basecalling position max_trace_signal. Then tracy accepts secondary peaks if they reach at least 0.33 * max_trace_signal for the default -p 0.33.