I can't find anywhere what 'NEGATIVE_TRAIN_SITE' means in a VCF data after VQSR. (I have searched everywhere on GATK) I thought it meant that the variant is considered to be not on the truth site due to bad VQSLOD scores, and should be filtered out. However, in my VCF data, the VQSLOD score and whether 'NEGATIVE_TRAIN_SITE' is True or False does not correspond. What does this term stand for? Thanks :)
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