I am currently taking an online tutorial on Galaxy and I have managed to complete some of the steps. However, the last one demands working with the final VCF file to determine the amount of SNPs, INDELs, MNVs, etc. I have no idea how to do that. I have already tried a few things googled a little bit, but unfortunately, I haven't got anywhere. I also need to get the names of the genes with the largest number of polymorphic sites.
Any ideas on how to extract this information out of a VCF file? I have even tried with Excel! Although I know that isn't very professional... besides of being quite difficult and impractical to do (not to mention that not even then I have managed to filter this info).
Please any ideas? I will surely give them a try!