When running VariantAnnotator (gatk4 release gatk-126.96.36.199), it still states " Warning: VariantAnnotator is a BETA tool and is not yet ready for use in production". Is there a plan to make VariantAnnotator a production level pro…
We tag duplicated reads in the BAM file. When we run GATK Coverage, will it filter out those deduplicated tagged reads? If not, how can we make GATK Coverage filter those reads out.