**5.8k**wrote:

I have some paired-end alignment data from BWA, and I am trying to use BreakDancer to call structural variants (well, more precisely, I'm trying to use SVMerge, which is a pipeline that includes a step using BreakDancer).

I think I've partially solved my problem by using Picard AddOrReplaceReadGroups to add a @RG line in the header (I no longer get an error message complaining about he read counts). This allowed the bam2cfg command to run for a lot longer (~12minutes, instead of failing immediately). However, the .cfg file is still empty.

I've looked at the breakdancer-help archive, but it looks like there are a lot of similar unanswered questions. So, I'm guessing this is a common problem.

I've tried running bam2cfg.pl with no optional commands as well as "-q 20" (to lower the threshold for the quality filter (although I wouldn't have expected this to be a problem). I noticed a lot of people ran bam2cfg.pl with the -g and -h parameters, so I also tried that. However, nothing is produced beyond an empty .config file.

In other words, here is my current command:

```
/opt/breakdancer-1.2/bin/bam2cfg.pl -q 20 -g -h file.bam > bd.config
```

This is my .bam file header:

```
@HD VN:1.4 SO:unsorted
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr1 LN:249250621
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chrM LN:16571
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@RG ID:1 PL:illumina PU:barcode LB:AGTGGT SM:4_AGTGGT
```

Does anyone know any other strategies for getting the initial bam2cfg.pl step to work?

**380**• written 5.2 years ago by Charles Warden ♦

**5.8k**