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AF in the final vcf
I have my final vcf file after variant recalibration and I was wondering where the AF information comes from.
I suppose it comes from the training data. Right?
I am asking because I have too many variants with AF=1.00 or AF=0.00. and what I want is to extract the variants that have AF<0.15 according to the 1000 genome.
Can I do this through GATK? is the AF in my final file what I should be based on to do make the filtering?
Look forward to your reply.