local de novo assembly and split-read alignment at known sites and output bams?

Question

[lyz10302012]

Given a set of candidate snvs and indels, is there any tools to be able to perform local de novo assembly and split-read alignment and output small bams (correct bams after assembly or split-read alignment) at these selected sites?

[Devon Ryan]

Do you really need assembly or just local realignment? The later can be done with GATK and probably does exactly what you want.