Hello,

I am using GATK 3.8 and want to call variants in GVCF mode:

gatk3 -T HaplotypeCaller -R human_g1k_v37.fasta -I test.bam -ERC GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -o abc.vcf -L region.sort.bed -A QualByDepth

However, no QD values show up and in the VCF header it says:

excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth]

It seems like the excludeAnnotation has priority over the -A arguments. Do you have any idea how to avoid excludeAnnotation?

Best,

Andreas