Test-drive the GATK tools and Best Practices pipelines on Terra
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VariantAnnotator and multiple records in resources
I'm using VariantAnnotator to add annotations to variants from a bunch of sources. One issue that I have is that for some variants, there are multiple annotations in a supplied resource. In the docs, I read
"Note that if there are multiple records in the resource file that overlap the given position, one is chosen randomly."
Can this behaviour be altered? I need to output all annotations for a record, either on a single line, or on multiple.
In the case i'm working on, one line has the annotation "CLNSIG=5" (i.e. a known pathogenic variant) and the other (likely older record) is "CLNSIG=1" i.e. a variant of unknown significance. I need to output both so I can filter downstream (using SelectVariants) to select those where "CLNSIG=5".