In workflows using a reference sequence (e.g., the Variant analysis workflow) “P not Ref” is the probability that the base does not match the reference. The P not Ref cutoff can be set using a variety of methods, including both “hard” and “soft” filters. The following table describes the wizard parameters and their corresponding scripting commands that relate to P not Ref filtering.

SeqMan NGen Wizard option Scripting command equivalent Notes
Advanced Assembly Options > Variant tab > P not ref parameter Command:
assembleTemplate
computeSNP
loadBAM
or setParam

Parameter: snp_minProbNonrefToCall
This is a “hard” filter. Data not matching the criterion are permanently removed from the assembly.

In the unusual case that the hard filter (see above) is missing, computeSNP > snpFilter > pNotRefMinVal is used to set the minimum value that can be displayed in the SeqMan SNP table.
Assembly Options screen > SNP filter stringency radio buttons Command:
computeSNP

Parameter: snpFilter

Property: pNotRef
This is a “soft” filter. Data not matching the criterion are removed from the default display of the SeqMan SNP table.

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