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.
What does an error message mean?
This document lists error messages that you may encounter when using Oncotator. For each, you will find an explanation of what the error message means, and how to solve the problem (if possible).
Entrez Gene ID was zero, but Hugo Symbol was not Unknown
Problem: The current GENCODE datasource does not have a complete list of the Entrez Gene IDs.
Solution There is no solution yet. This is a known issue and will be solved in a future release of the default datasource corpus.
oncotator.DuplicateAnnotationException.DuplicateAnnotationException: 'Attempting to create an annotation multiple times
Problem: This occurs when Oncotator is being directed to create the same annotation on a mutation, but each with different values. Typically, this is caused by a maflite/tsv input file with redundant columns. For example, "Start_Position" and "start". Oncotator does use aliases, so the annotation could have different column header text, but be regarded as the same annotation.
Solution: You need to clean up the columns in your input file to avoid such conflicts.