I am looking at some genotype data for some pooled DNA with a sample size of 10. The data is in dibayes format and for each snp tells me the coverage of that snp, the number of times the reference allele was counted and the number of times any other alleles were counted.
As an example one SNP had 7x coverage and was the minor allele was seen 1 out of 7 times and the major allele was seen the other 6.
How do you work out the minor allele frequency for this population. There are 20 chromosomes present but we've only seen 35% of them (7 out of 20) so we can't simply say the MAF is 14%
Also other SNPs may have higher or greater coverage and I presume you need to account for that somehow too.
I would ultimately like to create a simple allele frequency spectrum. I've had a look for some information on this but all the papers i have seen are way too complicated for what i need. Can anyone recommend a basic introduction to this analysis?
thanks a lot