In reference-guided workflows, “P not Ref” is the probability that the base does not match the reference. The P not Ref cutoff can be set using “hard” and/or “soft” filters. The following table describes the wizard parameters and their corresponding scripting commands that relate to P not Ref filtering.
In a “hard” filter, data not matching the criterion are permanently removed from the assembly. To set a hard filter, use the P not ref parameter located in the Variants tab, accessed by pressing the Advanced Analysis Options button in the Analysis Options screen.
In a “soft” filter, data not matching the criterion are removed from the default display of the SeqMan SNP table. To set a soft filter:
- In the wizard – Use the SNP filter stringency radio buttons in the Analysis Options screen.
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