How are consensus sequences generated, after breakpoint groups extracted?

[thename...@gmail.com]

Dear SMuFin team,

I am wondering how consensus sequences are generated after extraction of the breakpoint groups containing both non-mutated and mutated alleles. It seems like, the reads within each breakpoint group must be aligned against each other to correctly generate the consensus sequence.

If so, which alignment tool is used? If alignment is not necessary, would you mind briefly explaining how this is performed?

I suppose if alignment is being used your using samtools mpileup?

Very Kind Regards :D

Izaak