I think that adding the possibility to provide the --maxVariantFrac option (and its --minOppositeDepth counterpart, by default set to 0) would be of great value.
The possibility to switch on and off --keepDupes (currently by default properly being on) would also be useful to account for current EM-seq library preparation technologies that produce complex libraries that have low probability of fragments having the same start and stop positions unless they are true duplicates
Description of feature
Hi all,
I think that adding the possibility to provide the
--maxVariantFrac option(and its--minOppositeDepthcounterpart, by default set to 0) would be of great value.The possibility to switch on and off
--keepDupes(currently by default properly being on) would also be useful to account for current EM-seq library preparation technologies that produce complex libraries that have low probability of fragments having the same start and stop positions unless they are true duplicates