eldariont/svim

Improved Documentation

Closed this issue · 2 comments

CharlesARoy commented

Thanks so much for developing this tool and making it accessible to the research community!

As I was getting started with SVIM I noticed that in the example analysis you use options like --interspersed_duplications_as_insertions and --max_sv_size 1000000. I've tried to find a place where all options are listed (e.g. with svim --help) along with a description of what they do, but I haven't been able to find one. Does such documentation exist?

Thanks for your help!

eldariont commented

Hi Charles,

first of all, I'm very sorry for my long reply time.
To list all the options of SVIM along with their description you can use svim alignment --help or svim reads --help depending on which mode of SVIM you use. svim --help only gives you a general overview of the two modes so that's why it didn't return what you where looking for.

I hope this does not come too late and is of help. Let me know if you have any other questions.
Best
David

CharlesARoy commented

Thanks very much, that's exactly what I was looking for!

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