wgsim outputs different files

Question

[signauncreal]

Hey guys,

I'm simulating SVs on the human genome using svsim. The output files I'm using with vgsim to simulate sequencing reads. I have observed something I cannot make sense of:

depending on whether I use svsim in contig or whole genome mode, the result I get using wgsim on either files differs from each other. Shouldn't both output files from wgsim be completely identical?

Can you guys help me out?

Answer 1

[iraun]

From the SVsim manual:
"The default mode is called contig mode. In this mode, the fasta file will contain only small regions of the genome surrounding the target location or breakpoints of the SVs. The other major moade is called Whole Genome Mode (WGM). In this mode, the entire mutated genome is output to the fasta file."

So, according to the above paragraph, the fasta output file that SVsim generates depends on the mode. And as the fasta file changes, the reads that you are generating using wgsim will change too.

Answer 2

[signauncreal]

that is true, but the files give out the same information, just a marginal portion (roughly 5%) of the information given in the file originating from svSimContig is missing in the file given from svSimWG. That is not expected given the information you just stated. Anyways, what im trying to emphasize is that both output files, given they have the same format, should not differ from each other (if not stated otherwise in the documentation of wgSim).