Hi

I'm using the RSVSim package to simulate structural variants in a genome. When simulating translocations it works fine with up to around 10, but when trying to simulate 20 or more I get an error. Does anybody know if and how it is possible to create more translocations in RSVSim or if there is an absolute maximum at around 10.

The command I use is:

sim = simulateSV(genome=genome, dels=50, invs=50, dups=50, trans=100, sizeDels=sizeDels, sizeInvs=sizeInvs, sizeDups=sizeDups, percSNPs=0.1, bpFlankSize=50, repeatBias=TRUE, repeatMaskerFile="hg19.fa.out", seed=223456)

and the response I get when running:

Calculating coordinates: 100 translocations
  |========                                                              |  12%

Error in sample.int(length(x), size, replace, prob) : 
  invalid first argument
Calls: simulateSV ... simulateSV -> .simTranslocationPositions -> sample -> sample.int

Hi!

In RSVSim, translocations mean the exchange of whole chromosome arms. Hence, their number is limited by the number of chromosomes (max 12). You may have a look at the "insertions" parameter, which simulates the insertion of one chromosome fragment into some other place (it either copies the fragment or cuts it out). If you don't like the fragment and insertion point to be chosen randomly, you can also specify the exact coordinates. I'm also planning to insert custom sequences, but this is still on my todo list (sorry).

Hope that helps and does what you want!

Thanks for the quick answer. I'll take a look at insertions then. It looks like that could work for my purposes.

Also, thanks for a useful tool. :)