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UnifiedGenotyper : -1 does not represent a valid base character

sletortsletort franceMember

Hi, I suppose I had a problem with my bam file, but I don't know what I should look for.

Any help appreciated.

ERROR stack trace

java.lang.IllegalArgumentException: -1 does not represent a valid base character
at org.broadinstitute.gatk.utils.genotyper.DiploidGenotype.createDiploidGenotype(DiploidGenotype.java:115)
at org.broadinstitute.gatk.tools.walkers.genotyper.SNPGenotypeLikelihoodsCalculationModel.getLikelihoods(SNPGenotypeLikelihoodsCalculationModel.java:177)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoods(UnifiedGenotypingEngine.java:305)

cf attached file for complete stack.

Answers

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