AB large InDel Tool (v1.0), which identifies deviation in clone insert size, was used to detect large indels from SOLiD reads. Indels were supported by at least two clones (cluster of reads) and a distance deviation greater than 6 s.d. from the normal distribution of insert size. Breakdancer45 was used to detect large structural indels (100–100,000 bp) from Illumina reads. The distribution of insert size from high quality (>35) paired-end reads was computed, and those greater than 6 s.d. from the mean were used to define large indels. A minimum confidence score of 90 was used by BreakDancer. All clones that deviated by more than 100 kb were discarded for both methods.
