I'm new to this field and was wondering what exactly it means to find the intersection, complement and union of .vcf files. Related to this, is why would you want to perform these actions? If there is a tutorial on this I would be interested to know it. Any responses would be appreciated.
An intersection means that a particular object (in this case a SNP) belongs to both sets. A union would be an object that belongs to one or the other set. The complement is what is not in the first set but in the second set.
You would want to do these types of analyses to compare conditions of samples that you have SNPs for.