The P not Ref cutoff can be set using a variety of methods, including both “hard” and “soft” filters (see table). The following table describes three of the SeqMan NGen scripting parameters/properties that relate to P not Ref filtering, along with their equivalent Wizard parameters.
|
Scripting command |
SeqMan NGen Wizard equivalent |
Notes |
|
Command: assembleTemplate, computeSNP, loadBAM, or setParameter Parameter: snp_minProbNonrefToCall |
Advanced Options > SNP Options tab > P not ref parameter |
This is a “hard” filter. Data not matching the criterion are permanently removed from the assembly. |
|
Command: computeSNP Parameter: snpFilter Property: pNotRef |
Assembly Options > SNP filter stringency radio buttons |
This is a “soft” filter. Data not matching the criterion are removed from the default display of the SeqMan SNP table. |
|
Command: computeSNP Parameter: snpFilter Property: pNotRefMinVal |
N/A |
In the unusual case that the hard filter (see above) is missing, pNotRefMinVal is used to set the minimum value that can be displayed in the SeqMan SNP table. Otherwise, this parameter is ignored. |