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probelm with Variant Annotations

aditiskaditisk Ann Arbor Member

I am trying to use Variant Annotations in my joint variant calling step. I am using many of them but just two of them have some issue and are not working. I have attached the screenshot below. I am using the 3.3-0 version of GATK. Could you please tell me why just these specific ones are giving me issues ?

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    It looks like you have either too many spaces or a new line between the annotations. For example, the command should be something like java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R $ref -I $bam -o $vcf -A annotation -A annotation

    I hope you can fix it!


  • aditiskaditisk Ann Arbor Member

    For joint calling the inputs are supposed to be individual vcf files generated using the Haplotype caller right ? In your comment above you have mentioned that a bam file is the input. Could you please clarify that ?

  • aditiskaditisk Ann Arbor Member

    I also tried retyping my entire command and the spaces or new line character does not seem to be a problem. Only the two specific annotations are causing trouble.

    I removed those two annotations and the command seems to be working at least for now. Could you please explain why those 2 annotations are causing a problem ? Thanks a lot :smiley:

  • aditiskaditisk Ann Arbor Member

    Thanks a lot for your quick response.

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