GATK - Fun - Confusion - Fear - Frustration - Things to Remember
Post date: Jan 9, 2013 8:23:34 AM
There are many great things about the GATK software, primarily their excellent level of support, but somethings are a bit irritating like "we change it all the time so check the --list function" which requires you to prep up a complete GATK command which can be difficult when you have no idea what you are doing.
So here are the lists I'm always wanting to have on my wall (The Genome Analysis Toolkit (GATK) v2.3-4-g57ea19f)
Variant Annotator List of Annotations
Standard annotations in the list below are marked with a '*'.
Available annotations for the VCF INFO field:
Available annotations for the VCF FORMAT field:
Available classes/groups of annotations: