Breakdancer-max command not found during SV detection

Question

[Hasib]

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?

Answer 1

[ATpoint]

In the folder:

./program

Or anywhere

path/to/program

or put into PATH

[Hasib]

It worked. Thank you so much!