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Hi GATK team!
I have a question.
I want to compare my two VCF files for checking the discordance.
Reading the GATK Forum, I picked up picard Genotype Concordance.
I can get the metric files, but I can't create the output vcf file with the argument of OUTPUT_VCF=true.
I received the message :
Exception in thread "main" java. lang. IllegalArgumentException: Duplicate allele added to VariantContext: CA*.
I don't understand the message.
Please tell me how to solve this problem, or to teach another way.
I use picard/2.9.2