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UnifiedGenotyper : -1 does not represent a valid base character

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(

cf attached file for complete stack.


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