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?