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Questions - gatk

Error running gatk HaplotypeCaller with allele specific annotations

I've got HaplotypeCaller working nicely in standard mode, like so: # Run haplotypcaller gatk --java-options "-Xmx4g" HaplotypeCaller \ --intervals "$INTERVALS" \ -R &qu...
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Mike

variant

gatk

Votes: 0

Answers: 1

Latest Answer

I think that those options should be: -G StandardAnnotation -G AS_StandardAnnotation At least, when I changed them to that, it didn't throw an error message. However, I haven't used GATK much, so I'm...
test-img

Josh Burdick

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