Has anyone been able to figure out how to get breakdancer_max to run with the -o flag? Everywhere I've looked people have posted this same issue and I haven't seen any response to get it working and the devs don't respond to the issue, it's very frustrating.
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I have not gotten the -o flag to work at all. At first, it could not read my bam file index (because I did not have one). Once I solved that I tried running it with -o 17 or -o chr17.
Neither produced a result. No errors, just made empty files. For the moment I am stumped.
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I got -o to work in breakdancer-max1.2, apparently they fixed it there. However there are many unknown (UN) svs called and for some reason running each chr individually then running in -t mode is magnitudes of order faster than running the entire bam without -o or -t which is rather shocking.
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Interesting. Good to hear the issue is resolved.
It appears I will not be able to get their latest version because of the methods they describe for installing it. Very frustrating. Maybe if I ask my computing admins very nicely they will do it for me...
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