Where can I find more information about delly's command line options?

[Marc Perry]

Hi Tobias,

As I mentioned I am trying to use the docker version of the pcawg_delly_workflow from Dockstore but when I was comparing the actual commands that they use in that image to launch the various delly jobs I noticed that there are command line options that don't seem to be documented or referenced in your own GitHub repo for what is now called DELLY2.  For example:

-s 9

-q 1 

-p delly_results/delly/run_id.deletions.pe_dump.txt 

Are all examples of "extra" flags set inside the running docker container.  I realize that they were running delly v0.6.6 whereas your own GitHub repo is now up to delly v0.7.5 but is that the only difference? That those options are no longer available with the newer version?  When I try the delly --help command it doesn't explain how to get a detailed listing of all the options and their uses, nor could I find that described anywhere.

Thanks,

-- Marc Perry

[Tobias Rausch]

Hi Marc,

These options are available you just have to use 'delly call' to discovery and/or re-genotype SVs.

I have introduced sub-commands as in samtools to accomodate additional programs to merge and filter SVs.

The only option that indeed does not exist anymore is -p to dump all paired-ends. The main reason is that this option was slowing down Delly a lot and also makes little sense by now because Delly also calls SVs from soft-clips alone (without paired-ends). 

Best, Tobias

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