If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

How to narrow down the variants after VQSR in germline variant discovery and filtering?

theomarkertheomarker qingdaoMember
edited April 2018 in Ask the GATK team

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?




Sign In or Register to comment.