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Using Sitesonly vcf to add annotations

Dear GATK Team,

I observed in Jointdiscovery.wdl that VQSR is run on sites only vcf instead of vcf with genotype & samples.
Can we do the same to add annotations to sites only vcf with 1000g, gnomad?
If is is possible. How can I merge annotated sitesonly.vcf with actual vcf which contains genotype for all samples?

Please help me to resolve this?

Thanks In Advance
Fazulur Rehaman

Answers

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