See http://www.gen2phen.org/wiki/tools-and-methods-mapping-genomic-structural-variation (see bottom page for suggestions)
I would recommend delly as well (is not in that list):
Assembly is the best way to access insertions. Various approaches, either
- Global variant assembly. Here's the paper where this approach is introduced:
"De novo assembly and genotyping of variants using colored de Bruijn graphs." Z Iqbal, M Caccamo, I Turner, P Flicek, G McVean, Nature Genetics (2012)
a)Cortex will do this http://cortexassembler.sourceforge.net/index_cortex_var.html
b) So will SGA https://github.com/jts/sga
- Local assembly by taking reads from a bam
a) There are versions of these using SGA and Cortex (the latter is called Platypus) being used in the 1000 Genomes project, you could ask Jared Simpson at the Sanger Institute or Gerton Lunter at the Wellcome Trust Centre for Human Genetics in Oxford about those. Both of these show a lot of promise.
b) Brad Chapman at EdgeBio has incorporated local Cortex assembly into CloudBioLinux http://bcbio.wordpress.com
c) The Broad have recently started providing local de novo assembly in GATK, but not sure it will do many >100bp calls.