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.
- Realignment of unaligned ends
- Guided Realignment
- Multi-pass local realignment
- Known Limitations
- Computational Requirements
- How to run the Local Realignment tool