Error in VariantAnnotator

Because my reference is in scaffold level and GATK not designed to analyse such referenes, thus my variant caller project done using samtools. Now i want to add QD(qualityofdepth) to vcf files using VariantAnnotator but i get error as following:

ERROR MESSAGE: Invalid command line: Argument annotation has a bad value: Annotation QD was not found; please check that you have specified the annotation name correctly

my used command:

java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R /home/mylinux/refdic/DROMREF.fasta -I /home/mylinux/Drom1/realigned_D1.bam -V /home/mylinux/Drom1/variants/SNPSwhitGQ.vcf -L /home/mylinux/Drom1/variants/SNPSwhitGQ.vcf -A QD -o /home/mylinux/Drom1/variants/GATKANN.vcf

how can i add QD to vcf file?


  • i fixed above mentioned error by using -A QualByDepth but i get another error:

    ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '13'

    i used that reference for local realigning in GATK and it worked well but now it give error. what happend?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That typically happens when your reference file was edited or saved on a Windows machine because of character encoding differences. See previous threads on this topic for help with resolution.

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