I would like to extract sequence of reads from a bam file in such a way that indels are also incoproored based on information obtained from flags/penalty information. Basically I want something like pairwise sequence alignment of all my reads ..1,2,3...N against my refence sequence of interest . (Just imagine each row is a read from Sam/bam file obtained after alignment of data) and showing wherever a deletion was present as '-'. Insertion as read adjusted according to reference.
Do you know any Unix or R based tools?
Thanks in advance