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 narrow down the variants after VQSR in germline variant discovery and filtering?
Hi GATK team,
I followd the gatk best practice for germline variant detection based on 100 WES samples. After
VQSR, I got a VCF file, which is 39G in size (Actually, I think it seems too much). However, the other company offers me a text 430 thousands variants (snv + indel) after filtering. Since I am not sure how they processed or filter variants, can anyone tell me how to filter, refine and annotate to get a analysis ready VCF?