VCF INFO AC field for failed snps

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5.7 years ago

steven.davis ▴ 10

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

VCF • 1.9k views

ADD COMMENT • link updated 4.5 years ago by Biostar 20 • written 5.7 years ago by steven.davis ▴ 10

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Hello steven.davis ,

what you are showing is not valid vcf file. So the question is, do you have a valid vcf file (than show us) or does your file looks like you are showing here?

fin swimmer

ADD REPLY • link 5.7 years ago by finswimmer 16k

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