I'm curious to know if anyone is currently using Staden as part of their mutaion detection scheme?
I have a good deal of experience with the package as a sequence editor, but am new to the mutation detection world.
Specifically, I'm curious what set of pregap4(v1.4+) modules are used [The documentation mentions some which appear to have been split apart, deprecated, etc. So I'm worried I'm missing someting].
I'm working on getting this series working:
Est Base Accuracies
Init Exp Files
Aug Exp Files
Ref Traces & Seqs
Anything missing? Is the order problematic? Any current docs I should be aware of?
john [major -at- cbio -dot- mskcc -dot- org ]
Firstly if you use Phred then disable the Estimate Base Accuracies section as it will overwrite Phred's scores. EBA exists purely as a "poor mans Phred" to allow good quality clipping without having Phred.
Secondly the Mutation Detection module uses the tracediff program and Het Indels uses the hetins program, both of which have been superceded by the single mutscan program (the Mutation Scanner module). However in some cases it may still work better - I'd say that it's worth experimenting with your data to see what gives the best results.
As I recall though if you use tracediff instead of mutscan then you don't need to use the Ref Traces & Seqs module, but I may be wrong on that. It's been too long to recall well.
As for who uses it... no idea. Hopefully someone else out there can make themselves known :-)