Test-drive the GATK tools and Best Practices pipelines on Terra
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Interpreting Allele frequency equal to 1.0
In the following vcf file, the AF allele frequency of ALT allele is 1.0. Does it mean that it is not a true SNP of interest? Does it also mean that ALT allele always occurs and REF allele never occurs in the population?
Also not sure how allele count AC=37 is being calculated.
Chr1 pos=565286, REF=C, ALT=T, Info AC=37; AF=1.0 Format GT:AC:AF:NC Child=1:11:1.0:+T=4,-