Hi everyone!
I need to find certain SNPs beetween my fungal genomes. I checked the https://github.com/ekg/alignment-and-variant-calling-tutorial and the https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/dip/tutorial.html tutorials. I had problems with the first one and couldn't finish it. But it seems, that one is more punctual/detailed then the second one (I finished it). The VcfAllelicPrimitives and the SnpEff tools give me the same result, like the other tools in the first tutorial (for example: VcfFilter)? Or can somebody explain me, how can I specify the parameters in the second method (I mean which sights, tell me how to configure the softwares, for example: inn SnpEff:at the Set size for splice sites (donor and acceptor) in bases; how should I know which set size is optimal for me)?
Thanks for your support in advance!
