GATK 4.3.0 VQSR

Question

[wonde2000]

Hi all, With GATK4.3.0 I try to use VQSR and I got the error message. Based on GATK tem recommendations, I ran "VariantRecalibrator model" to fix the error https://gatk.broadinstitute.org/hc/en-us/articles/9570271608219-VariantAnnotator. However. the error message still persists. Is there any other way to fix such problem? Thanks!

A USER ERROR has occurred: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.

Answer 1

[Pierre Lindenbaum]

you're using INFO/QD as a data in your VCF to train the recalibration model but no variant contains this INFO/QD

[wonde2000]

Dear Pierre Lindenbaum, So, is there any way to fix and proceed the SNP calling process? I am quite new for such kind of analysis.