How to simulate SV (insertions and deletions) with length > 50bp?

[Meltpinkg]

Hello! According to the help page, when randomly simulateing variants, simuG can simulate SNP/Indels (1~50bp), and SVs (CNV/inversion/translocation). How can I simulate random insertions and deletions which are larger than 50bp? Thanks!

[yjx1217]

Hi @Meltpinkg ,

Technically, an insertion or deletion larger than 50bp will be considered as SV-level insertion or deletion, which can be simulated via CNV simulation.

Or, you can change the line 1620 of the simuG.pl script to replace $indel_size=50 with $indel_size=M, where M can be whatever the maximal value of the INDEL that you want to simulate.

Best, Jia-Xing

[Meltpinkg]

Hi @yjx1217

Thanks very much for your reply. That helps me a lot! :)

Best, Shuqi

[yjx1217]

Great it helps! You are welcome. :-)