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Methods to filter mutation predictions #41

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
For Syn data and others add a way to change the prediction threshold for SNPs 
and microindels. By score or by coverage. Somewhat redundant with other 
post-processing tools (for VCFs for example).

Original issue reported on code.google.com by jeffrey....@gmail.com on 31 May 2012 at 8:46

GoogleCodeExporter commented 8 years ago 
("polymorphism-score-cutoff", "Log10 E-value cutoff for test of polymorphism vs 
no polymorphism", 10, ADVANCED_OPTION)

That option is setting the settings.polymorphism_log10_e_value_cutoff already.

Do you want another option for setting the 
settings.mutation_log10_e_value_cutoff value?

Original comment by Geoffrey...@gmail.com on 31 May 2012 at 10:34

GoogleCodeExporter commented 8 years ago 
Yes. Add this:

("mutation-score-cutoff", "Log10 E-value cutoff for base-substitution and 
micro-indel predictions", 10, ADVANCED_OPTION)

Change the 10 to whatever the current default is in Settings.cpp.

Original comment by jeffrey....@gmail.com on 1 Jun 2012 at 1:02

GoogleCodeExporter commented 8 years ago 
This issue was closed by revision cc27e51c6613.

Original comment by Geoffrey...@gmail.com on 1 Jun 2012 at 6:28