Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

"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 ------------------------------------------------------------------------------------------

Answers

Sign In or Register to comment.