local de novo assembly and split-read alignment at known sites and output bams?
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?
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Devon Ryan
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lyz10302012
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lyz10302012
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Do you really need assembly or just local realignment? The later can be done with GATK and probably does exactly what you want.