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van den Berg authored
When GATK emits all sites, homref sites get the RQC annotation instead of the QC annotations. For vtools, these two annotations are used interchangeably, since they both contain genotype likelihoods. See the detailed explantation at https://gatkforums.broadinstitute.org/gatk/discussion/5115/haplotypecaller-genotypegvcfs-and-vqsr-for-alternatives-in-dbsnp
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