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VariantAnnotator not generating AlleleBalanceBySample

Hi GATK Team,

I am trying to have AlleleBalanceBySample for each sample for a pre-generate vcf file. But I am not getting it. Bellow is my command. Am I doing something wrong??

java -jar GenomeAnalysisTK.jar -T VariantAnnotator -R ../Genome/hg19.fa --variant all.vcf -o annotate.vcf -A AlleleBalanceBySample -L exome.interval.list

I am having it in the heading lines

FORMAT=<ID=AB,Number=1,Type=Float,Description="Allele balance for each het genotype">

But not in the formate field.

Best Answer


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