Breakdancer input inquiry

[moldach]

Using the most recent release of BreakDancer, version 1.4.5, generates several files (none of which are .txt files):

470.cfg
470.ctx
470.ctx.xyz.1.fastq
470.ctx.xyz.2.fastq
470.new.bam
470.new.bam.xyz.insertsize_histogram
470.new.bam.xyz.insertsize_histogram.png
470.sam

However, in the Mavin Tutorial the breakdancer-1.4.5 folder has several .txt files - one for each chromosome and a translocations file; e.g. chr1.output.txt and translocations.output.txt

How were these generated?

I thought Breakdancer fell under "supported tools since it was covered in the tutorial and mentioned in the documentation; e.g.

Some native tool outputs are supported and have built in methods to convert to the above format

[creisle]

Hi @moldach Its been a while since we've used breakdancer (its not one of our regular tools) however I've found the commands I used to run it. It looks like I created the text file by piping the output (the .txt format was just what we used, could be anything)

breakdancer-max -o <CHR> breakdancer.cfg > output/results/chr<CHR>.output.txt
breakdancer-max -t breakdancer.cfg > ouput/results/translocations.output.txt

I think in your case this is the .ctx file?

[creisle]

@moldach were you able to use breakdancer?

[moldach]

Hi @creisle it has been a while... my thoughts are no. However, I'm happy to re-visit my notes and try this out soon to help you improve the docs.

My apologies, but I had stepped away from SV-viz tools for a while to attend to other pertinent matters. We needed to come back to mavis for a manuscript one of the post-docs is preparing; however, we're having a problem with https://github.com/bcgsc/mavis/issues/229 at the moment which is more pressing.

Thanks for understanding

[liliailham]

Good evening, I have an issue to generate breakdancer-max -h And I get this return: breakdancer-max: command not found I an struggling to resolve the issue, but fortunately I couldn't ! so, any help please!

Thank you for understabding

[creisle]

Good evening, I have an issue to generate breakdancer-max -h And I get this return: breakdancer-max: command not found I an struggling to resolve the issue, but fortunately I couldn't ! so, any help please!

Thank you for understabding

@liliailham the SV callers are not installed as part of the MAVIS install. Have you installed breakdancer? The above error means the tool executable is not on your default path. If you have installed breakdancer you may be able to resolve this issue by giving an absolute path ex. /path/to/where/you/installed/breakdancer-max or by using environment variables to export the folder containing the breakdancer executable to the default path (assuming you are using some linux/unix based system).