the Allele Count (AC) tag is incorrect
Posted in Ask the GATK team | Last updated on 2013-02-25 17:24:53


Comments (12)

I am facing this error, when I try to validate the variants (ValidateVariants) of a vcf file which is produced through GATK just after UnifiedGenotyper. I am using GenomeAnalysisTK-2.3-6-gebbba25 and dbsnp_137.hg19.vcf. These variants are annotated by DepthOfCoverage, aplotypeScore, ,InbreedingCoeff and LowMQ ...

Basically, I generate two VCF files using UnifiedGenotyper separately, one for SNP and the other for INDEL.

the error for both is about the Allele Count (AC) tag: ##### ERROR MESSAGE: File F93.snp.vcf fails strict validation: the Allele Count (AC) tag is incorrect for the record at position chr1:1225579, 1 vs. 1

I appreciate your comments,


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