For my project I need to get copy numbers from single-end GBS data with reads mostly being 90bp in size. I have a reference genome with chromosomes etc. as well. I aligned the GBS data against this and generated 630 bamfiles.
I need to know the sizes of the copynumbers and their locations. I tried to look for tools and came across Control-Freec and CNVnator, as these tools didn't require paired end data. The results looked odd for cnvnator because the copynumbers varied wildly amongst my 630 Snapper fish BAM files (one 10000 the other 200), which is impossible due to them being from the same hatch. Control-Freec produced somewhat similar results, but I couldn't find the specific copynumber sizes from the results.
Anyone got recommendations for tools or parameters? GBS isn't used often and I can't find literature that even attempts this. Which is good as this is for my PhD project.
Thanks!
