Test-drive the GATK tools and Best Practices pipelines on Terra
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ASECounter vs AD and DP in vcf file
Dear GATK developer:
Can you please explain the difference between the allele counts obtained by running ASECounter and the allele read counts provided in the AD/DP fields in vcf file. It seems that the allele counts obtained by ASECounter is similar to DP the filtered depth in the vcf? while the AD calculation includes unfiltered reads?