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Breakdancer-max command not found during SV detection

Hi. I'm trying to detect Structural Variation (SV) in my Tumor-matched normal BAM files using the Breakdancer tool. I've installed and run the software according to the original paper's protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138716/) and have managed to produce the configure files using the bam2cfg.pl script so far. The next step tells to use the breakdancer-max program to process these configure files but when I'm running the command it says "breakdancer-max: command not found". It says the same thing even when I'm opening the terminal from the folder which contains the breakdancer-max program. How can I solve this?

sv detection breakdancer
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written by Hasib • Hasib

1 answer

In the folder:

./program

Or anywhere

path/to/program

or put into PATH

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written by ATpoint ATpoint

It worked. Thank you so much!

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written by Hasib • Hasib

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