Complex Indel Detection: A Simulation-Based Framework and Parsing with FreeBayes (opens in new tab)

In contrast to simple deletions and simple insertions, most complex indels involve both deletions and insertions, often with base changes within a few nucleotides of the indel's left and right boundaries. These complex indels often arise from double-strand breaks (DSB), which in normal somatic cells are predominantly repaired by nonhomologous DNA end joining (NHEJ). Such complex indels pose a difficult analytical problem for existing indel callers because the observed VCF representation may b...