problem with output of breakDancer

[pengyanbenben]

Hi all,

I'm running breakDancer for my samples and confused with the output file:

1. For the size of SV, there are positive numbers and negative numbers. What is the difference between them?

2. How do I know the SV sequence. For insertion (INS), the output file didn't provide any sequences. While for deletion (DEL), the SV size is different from the distance between the two break points, such as:

scaffold_8 2027151 4+0- scaffold_8 2027242 0+4- DEL 75 99 4 ./test_BWA/aln_A13.sorted.bam|4 0.21 1.58

the distance between two break points should be (2027242-2027151)=91, while the indicated size is 75. How do I know the exact deletion sequences between the two break points?

3. I output the BED files with option -g. Could anyone understand the BED file?

Any help would be greatly appreciated!!

Yan

[demienx]

Concerning your first question, my opinion is the positive length stands for deletion and the negative for insertion.