Do you know which software available on Galaxy is capable of performing structural variant analysis, for large insertions, deletions, inversions, translocations, etc.
I found under the tab, NGS:Variant Analysis, a few programs for variant analysis, except these deal with a smaller scale like SNPs and indels. I am unsure if those software algorithms are able to detect inversions or other structural variants.
I have tried using software for structural variant analysis from the command line. Pindel, LUMPY, breakdancer , SVDetect, but I am having issues with compiling and building them from source, even with the aid of Google, stackoverflow, biostars, and github, possibly because they were intended for use on UNIX or LINUX, and I am using Cygwin on Windows and an OS X.