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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.