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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
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!