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ccgd-profile / BreaKmer

A method to identify structural variation from sequencing data in target regions
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Where to start? #33

Open dsmarcoantonio opened 7 years ago

dsmarcoantonio commented 7 years ago

Dear BreaKmer team I just read the paper. It seems really promising your tool. However I can't find the documentation to set all things up. BreaKmer 0.0.6 has no documentation inside. Following the Issues tab I see some information, but how to set the breakmer.cfg? BLAT server...? Would be better to run locally? When one click on "Documentation" get into a loop to the same page. I appreciate any advice.

wollisonb commented 7 years ago

Hello,

You can run a BLAT server locally, which is what we do with success, but you need to point to it in the breakmer.cfg file. The breakmer.cfg file should contain the paths to the major BreaKmer dependencies as well as the specifics of the run such as the sample name and bam file path. The specifics are in outlined in BreaKmer/breakmer.cfg. Let me know if you have any more questions,

Thank you

ryanabo commented 6 years ago

Please see branched version: https://github.com/ryanabo/BreaKmer