What is the standard VCF INFO field, if any, to count the occurrences of variant genotypes having passed all filters?
Does AC count every occurrence of the alternate genotype, or only those occurrences where the call passes all filters?
Consider the haploid VCF snippet below. At position 300, the sample3 variant call does not pass all the filters. In this case, should AC be set to 1 or 2?
I need a field that counts only the variants passing all the filters. Should I invent something, use AC, or use some other standard field?
POS REF ALT INFO FORMAT SAMPLE1 SAMPLE2 SAMPLE3 100 A C,G AC=1,1 GT:FT 0:PASS 1:PASS 2:PASS 200 A C AC=2 GT:FT 0:PASS 1:PASS 1:PASS 300 A C AC=1 GT:FT 0:PASS 1:PASS 1:FAIL