BreakDancer

BreakDancer Pipeline

Step 1. Create a configuration file using bam2cfg.pl
e.g.,
```
myDirectory/bam2cfg.pl -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
e.g.,
```
myDirectory/BreakDancerMax.pl -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.