Attention:
The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 2019.

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

Sign In or Register to comment.