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AF in vcf files

There is some inconsistency in the community on how to calculate the AF (allele frequency) value in vcf files. GATK calculates a hypothetical value (0, 0.5 or 1 for normal diploid organisms). Other callers will calculate the AF as an Alt Allele Frequency.

Is there a way to have both values in the VCF file from GATK?

Best Answer


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