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Is it possible to recalculate QUAL on a subset of samples?
I have a joint-called VCF of 100s of samples in different pedigrees. For my analysis, I have to split the joint VCF into pedigrees. However, I would like to recalculate the QUAL scores for the pedigree VCFs.
I have GL/PL values and all other metrics GATK (v3) VQSR outputs. With these data, is it possible to recalculate QUAL for families that were joint called in a larger VCF?