GATK VQSR: recallibration using custom annotations
I have a VCF file that has several custom annotations(ABHet, blat score, etc) that I've added using bcf-annotate. I would like to re-run VQSR recalibration on this VCF file using those custom annotations. Is this possible or is recalibration allowed only using annotations generated by GATK e.g.: QD, DP, FS, SOR|MQRankSum, etc ?
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