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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?