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How many "-an" arguments in VariantRecalibrator should be used ?
I encountered a problem when using VariantRecalibrator function of GATK.
The following error often came out when I used the several common “-an” augments.
“##### ERROR MESSAGE: Bad input: Found annotations with zero variance. They must be excluded before proceeding.”
When I decreased the number of “-an”, another error came out.
ERROR MESSAGE: No data found.
I am confused about the “-an” argument. Which of them should be used?