Four tools were used to identify indels—Corona Lite small indels pipeline, MAQ, Pindel43 and BreakDancer44. Corona Lite was used to identify insertions of up to 3 bp and deletions of up to 11 bp using SOLiD sequence. Indels were further filtered by requiring at least three supporting reads, and indels within regions having extremely high coverage (1000 ×) were excluded. MAQ was also used to identify insertions up to 19 bp and deletions of up to 86 bp for 101 bp Illumina reads. A threshold of a minimum of three supporting reads and a minimum consensus quality of 30 was used. Rare heterozygous indels were discarded. Pindel was used to identify indels from 1 to 100 kb. Access to all of these variants is available on a custom version of the UCSC Genome Brower at http://ucscbrowser.genenetwork.org/cgi-bin/hgGateway.
