I am running GATK on bam file for variant calling. In the output file, I noticed that the Allele frequency is computed as 0.5 and 1.00.
What may be the reason for this?
Is it calculated correctly?
do you have only one sample ? the genotype is either heterozygous AN=2 AC=1 then AF=0.5 , or homozygous on ALT allele: AN=2, AC=2 then AF=1.0.
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