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How to extract annotation for a single sample after genotyping a combined gVCF file?
I have been running the GATK best practices for annotating numerous exome datasets. I have created gVCFs for each exome, combined into a single datafile, genotyped the datafile, and now have a combined .vcf file. However, each SNP has data for a variety of exomes. How can I extract a single exome's worth of annotation from this new .vcf file before running downstream VQSR filtering.