Associate Supporting Reads Of Fasta File With The Structural Variation

Question

[roalva1]

Hello,

I was wondering if there is any way to associate each supporting read of the fasta file (that you get with the -d option) with its structural variation. Let's say I have this deletion:

scaffold_1    44905    73+0-    scaffold_1    45119    72+76-    DEL    224    99    73    sample.bam|73    0.828015    0.34

This has 73 supporting reads, and I have a fasta file from the breakdancer output "reads.bar.1.fastq" and "reads.bar.2.fastq". Is there any way to associate them?

Thanks a lot!

Answer 1

[roalva1]

I figured out by myself, if you call breakdancer with -g option, you get a bed file with each supporting read associated to each sv.

Regards