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"GATK limitation: cannot genotype more than 500 alleles"

brantpbrantp Member
edited October 2012 in Ask the GATK team

GATK Team,

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?

Thank you!
Brant

Full stack trace follows; I can supply the relevant inputs and invocation if its helpful to be able to reproduce this error.

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: GATK limitation: cannot genotype more than 500 alleles
at org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods.getAllelePair(GenotypeLikelihoods.java:277)
at org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.chooseMostLikelyAlternateAlleles(ExactAFCalculationModel.java:92)
at org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.getLog10PNonRef(ExactAFCalculationModel.java:58)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateGenotypes(UnifiedGenotyperEngine.java:285)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:164)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:284)
at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:112)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78)
at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:246)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.5-25-gf46f7d0):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: GATK limitation: cannot genotype more than 500 alleles
ERROR ------------------------------------------------------------------------------------------

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