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Realignment
For every read that intersects a candidate alignment, the Strelka attempts to find the most probable alignments including the candidate indel and excluding the candidate indel. Typically, the alignment excluding the candidate indel aligns to the reference, but occasionally an alternate indel that overlaps or interferes with the candidate is found to be more likely. The indel caller uses the probabilities of both alignments as part of the indel quality score calculation, whereas only a single alignment (usually the most probable) is preserved for SNV calling.