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 are splice sites annotated?

LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev ✭✭✭

In Oncotator, the variant classification of SPLICE_SITE occurs when a variant is within two bases of a splice site on either the exon or intron side.

To determine whether a specific SPLICE_SITE is exon or intron, and to get the exact variant classification, use the secondary_vc annotation.


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