Local realignment

Local realignment is applied to existing read mapping data sets and aims to improve the alignment of individual reads in the presence of insertions and deletions (indels) relative to the reference. Improved alignment accuracy in regions containing indels is especially important for downstream analyses such as variant detection to reduce the number of false negative/false positive variant calls. Figure 25.27 depicts a typical read mapping that is improved by local realignment.

Image alignment
Figure 25.27: [A] The alignments of the first, second, and fifth read in this read mapping do not support the four-nucleotide insertion supported by the remaining reads. A variant caller might be tempted to call a heterozygous insertion of four nucleotides in one allele and heterozygous replacement of four nucleotides in a second allele. [B] After applying local realignment, the first, second, and fifth read consistently support the four-nucleotide insertion.