this is a very basic question but I can't find a proper explanation anywhere.. yes I have read the .vcf specification documents.
How are 'AC' and 'AN' calculated? I have human vcf files where there are homozygote variants with AC=2;AN=2 and heterozygote variants with AC=1; AN=2. If I had multiple samples with multiple variants, how are AC and AN calculated? So does AC ignore the reference allele? The vcf spec is not very helpful with "allele count in genotypes, for each ALT allele, in the same order as listed"?