Hi, I want to compare the Minor allele frequencies for a list of SNPs from my population with that of 1000 genomes all individuals MAF values. My aim is to get an appropriate p-value statistic to get variants having significant allele frequencies. How do I get started? Many thanks in advance.
I'm afraid that you don't know what the p-value is. The first thing about p-value is that it applies to populations, not to just plain numbers. If you have just two numbers (mean AF of your SNP vs. mean in 1kg database),then there is no discussion of having a p-value at all. Loosely speaking, the p-value says how much is the probability to draw samples in your population (of AF) if it came from other population (let's say of 1kg) - which loosely translates to how much your population (of AF of SNPs here) is different from other population (the 1kg AF, say) - the lower p-value means that the populations being compared are more certain to be different. You may find some useful posts on SE/SO regarding it, for example: https://stats.stackexchange.com/questions/166323/misunderstanding-a-p-value
Closing the discussion, if you need a p-value for your case, then you must have 1) either your whole population (=> the individual AFs in all samples, including 1kg) or 2) at least the mean and standard deviations of AFs.
BTW, what you need the p-value for?