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bcgsc / pavfinder

:mag: Post Assembly Variants Finder
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Example output files? #6

Closed stianlagstad closed 4 years ago

stianlagstad commented 4 years ago

Hi,

I would like to know if the output data that Fusion-Bloom produces can be used with https://github.com/stianlagstad/chimeraviz. Do you have any example output files that you can share?

Thank you!

readmanchiu commented 4 years ago

Thanks for your interest in Fusion-Bloom and sorry for the late reply. There is a compressed file of Fusion-Bloom output in the test directory: https://github.com/bcgsc/pavfinder/blob/master/pavfinder/test/transcriptome/expected_output/fusion-bloom.out.tar.gz After decompressing and extracting (tar xzvf), you can find the fusion output under the pavfinder folder. And as the name(sv.bedpe) suggests, it is a BEDPE format file, with the first three lines describing the version, command, and columns respectively. I don't think any of the fusion tools you supported uses the BEDPE format, but all the information should be in the output for you to, for example, generate a circos plot. Let me know if you need any more information, and I'm happy to write a parser for you if necessary.

stianlagstad commented 4 years ago

Thank you very much @readmanchiu ! I don't have time to look at it the first coming days, but I'll get to it :) I've created https://github.com/stianlagstad/chimeraviz/issues/85 on my end to track it.