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VQSR with missing annotation fields
I am calling variants (non-model organism) following the best practice workflow. After haplotypecaller (with GVCF) and GenotypeGVCFs, I want to perform VQSR (separately for SNPs and INDELs) to the raw vcf file (10 samples) as an alternative for filtering manually. As a resource I use a subset of very high quality variants (obtained with hard filtering, coming from different samples). However, I have noticed that not all annotation fields are present in the raw vcf file. For example, not all sites have a MQRankSum field, ReadPosRankSum field or MQ field. As I want to use these annotations for recalibration, I was wondering how the model handles such sites (I have been using GATK3.5 so far) and how this would affect the filter field.
I guess running variantAnnotator on the raw vcf file will not add the missing fields (for example ReadPosRankSum cannot be calculated when no reads are found with the reference allele).
Thanks a lot for your help!