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"GATK limitation: cannot genotype more than 500 alleles"
I'm running into a new error stating the following:
ERROR MESSAGE: GATK limitation: cannot genotype more than 500 alleles
I'm running with the default for --maxAlleles (which appears to be 3, consistent with several lines of output of the form "WARN 00:03:36,551 ExactAFCalculationModel - this tool is currently set to genotype at most 3 alternate alleles in a given context, but the context at agouti_bac:15111 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument "), so I suppose this is something else?
As an aside, is it possible to get a dump of the specific reference coordinate at which an error is thrown?
Full stack trace follows; I can supply the relevant inputs and invocation if its helpful to be able to reproduce this error.
ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: GATK limitation: cannot genotype more than 500 alleles