We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Picard GenotypeConcordance

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


Best Answer


Sign In or Register to comment.