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How to get a variant's abundance from calling file?
I'm wondering how to get a mutation's abundance based on variant calling result file. I noticed there is a 'AF' field in vcf file, but the value is always 1 or 0.5. It's different from the ratio of ref/alt reads in bam file. I also found that 'AD' filed in FORMAT column records the ref and alt reads count, but it can be different with corresponding reads number in bam file as well. So which field should I use to get variants' abundance? Thank you!