I have some breakpoint data and I would like to determine type / class of each rearrangement. I believe BreakDancer can do this.
Could someone please show me how a BAM file is formatted so I know if my data has enough information to be reformated for use with this tool?
Example of typical data -
Germline/Somatic Evidence #Solexa reads Chr L Pos L Strand L Chr H Pos H Strand H Microhomology length (bp) Microhomology seq Non-templated sequence length (bp) Non-templated sequence Somatic Seq 1 18 19092052 + 18 30289323 + 0 0
I already have a script which pulls back the sequence observed across a breakpoint if this is helpful.