faa9e4da_SnpEff__Message_type
[Code] W1 [Description / Notes] This means that the ‘REF’ field in the input VCF file does not match the reference genome. This warning may indicate a conflict between input data and data from reference genome (for instance is the input VCF was aligned to a different reference genome). [Message type] 
WARNING_REF_DOES_NOT_MATCH_GENOME
SnpEff
Message type