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 November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

Annotation, DNA vs RNA

hjkim123hjkim123 USMember
edited August 1 in Ask the GATK team

We have WES and RNA data analyzed through GATK pipeline.
All steps were smoothly processed but I noticed a difference between the two after annotation.
The WES data has about 7.7 million variants but 1.5 million variants (19%) are annotated to rsIDs.
The RNA data has around 5.2 million variants but 2.1 million variants (40%) are annotated to rsIDs.
Total number of variants for WES is greater, which is acceptable but the number of annotated rsIDs is half of that of RNA.
The same reference data, dbsnp_138.hg19.vcf, was used.
The variants do not need to be annotated to rsIDs but I am just wondering what possible reasons are for the difference. Any thoughts are welcome.

Thank you for any help.
Post edited by hjkim123 on


Sign In or Register to comment.