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nhansen / SVanalyzer

Tools for the analysis of structural variation in genomes
http://svanalyzer.readthedocs.io/
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Update SVbenchmark #5

Closed cjain7 closed 4 years ago

cjain7 commented 4 years ago

minor error in SVbenchmark manual

cjain7 commented 4 years ago

Also, knowing the default values would be useful here. Online documentation probably specifies incorrect default values. Please check.

nhansen commented 4 years ago

Thanks, Chirag. These parameters aren't so intuitive, and I did recently make them more stringent without updating the documentation (sorry!), which may be why you're getting lower stats. Probably worth trying the old values of normshift=1.0, normsizediff=1.0, and normdist=1.0. The maxdist parameter is probably good where it is, as increasing it really increases the running time.