I had annotated raw indel file (given by UnifiedGenotyper), 1000G_omni2.5.b37.sites.vcf and hapmap_3.3.b37.sites.vcf with all possible annotations including QD (QualByDepth) using VariantAnnotator. However, i got an error when i tried to run VariantRecalibrator. It was complaing that QD has not been found in training variant. Is QD important annotation for indel filtering. Can it be ignored ?
P.S. - i did not use sample bam file while annotating training data set.
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INFO 15:11:55,999 RMDTrackBuilder - Loading Tribble index from disk for file NCBI_dbsnp_for_GATK.vcf
INFO 15:12:21,650 TraversalEngine - chr1:128346793 1.98e+07 30.0 s 1.5 s 4.1% 12.1 m 11.6 m
INFO 15:12:51,650 TraversalEngine - chr9:130658800 5.26e+07 60.0 s 1.1 s 53.9% 111.2 s 51.2 s
INFO 15:13:13,618 VariantDataManager - QD: mean = NaN standard deviation = NaN
INFO 15:13:16,417 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-13-g1706365):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator
##### ERROR ------------------------------------------------------------------------------------------