BreakDancer Pipeline

  • Step 1. Create a configuration file using

    myDirectory/ -g -h tumor.bam normal.bam > BRC6.cfg

    bam2cfg now only has the perl version.

    Manually view the insert size and flag distribution results in BRC6.cfg to see if there are any data quality issue. Usually std/mean should be < 0.2 or 0.3 at most. The flag 32(x%), represents percent of chimeric insert, this number (x%) should usually be smaller than 3%.

    View png files for the insert size distribution. You should usually see a normal distribution, a bimodal distribution is undesirable and it is not recommended to continue BreakDancerMax step with this situation existing.

  • Step 2. Detect inter-chromosomal translocations

    myDirectory/ -t -q 10 -f -d BRC6.ctx BRC6.cfg > BRC6.ctx
          for perl version;
    myDirectory/breakdancer_max -t -q 10 -d BRC6.ctx BRC6.cfg > BRC6.ctx
          for cpp version.

    The -d option dumps CTX supporting read pairs into fastq files (in this case BRC6.ctx) by library.

    This step normally takes 12 hours or so for three bam files, 8 hours or so for two bam files for cpp version, around three days for perl version.