Dear all,
I am new to NGS and have been trying to run through the GATK variant calling pipeline on exome sequencing data. I'm currently having an issue with the variant quality score recalibrator, I have the following error message.
ERROR MESSAGE: Bad input: Values for HaplotypeScore annotation not detected for ANY training variant in the input callset.
Ive tried using using variant annotator on my UnifiedGenotyper vcf file, but that does not seem to correct the problem. I am also unsure as to whether my UnifiedGenotyper vcf file, or my hapmap, dbSNP and omni1000g resource files, are missing the annotations? Any help/advice on this issue would be much appreciated.
Thanks,
Elliott
I am new to NGS and have been trying to run through the GATK variant calling pipeline on exome sequencing data. I'm currently having an issue with the variant quality score recalibrator, I have the following error message.
ERROR MESSAGE: Bad input: Values for HaplotypeScore annotation not detected for ANY training variant in the input callset.
Ive tried using using variant annotator on my UnifiedGenotyper vcf file, but that does not seem to correct the problem. I am also unsure as to whether my UnifiedGenotyper vcf file, or my hapmap, dbSNP and omni1000g resource files, are missing the annotations? Any help/advice on this issue would be much appreciated.
Thanks,
Elliott
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