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Question: Question: Why BreakDancer does not displays the amount of reads supporting SV?

Bulbul
200 days ago

Question: Why BreakDancer does not displays the amount of reads supporting SV?

Using breakdancer the output consists of DEL, INV, INS, CTX and ITX. Using following commands:

bam2cfg.pl -g -h dis.bam normal.bam > config_file.cfg
breakdancer_max -d test config_file.cfg > dis_normal.ctx

the 11th output column should displays the amount of reads supporting the called SV per bam-file. I have some unusual research in 11th column, can you please helpme to fix it.


Answers
0

It does not work if you don't have set the read-group information correctly (as is said in the breakdancer documentation). But more importantly, if you filter your results for SVs were this 11th column says that the SV is only supported by reads of your dis.bam file it does not look very somatic if you view the results in IGV. Not for deletions (which I think are easiest to compare), not even talking about the others.

I think the best way to go is to run breakdancer on the two .bam files seperately and then use secondary tools to compare the results.

For Deletions, you can make 2 bed files for all locations that are deleted in your 2 bam files. Than you can use intersectBed from BEDtools to find the deletions in your tumor results that are not present in your control results:

intersectBed -v -f 0.5 -a dis_breakdancer_deletions.bed -b control_breakdancer_deletions.bed

For inversions, insertions, inter- and intra chromosomal SVs the situation looks slightly different to me. Here the breakpoints are of imporantence, not the location from start to end (like when looking at deletions). I think you should make a list of all breakpoints, use a buffer size (say +- 500 bps) and see which breakpoints are present in your dis and not in your control (maybe the same way using bedtools?)