snpEff 'WARNING_REF_DOES_NOT_MATCH_GENOME' during hg38 annotation

Question

[spiral01]

I have used snpEff to annotate 1000genomes phase 3 vcf files. However, I seem to be getting a large number of warnings that read: 'WARNING_REF_DOES_NOT_MATCH_GENOME'. Too many of these warnings indicate a lack of match up between vcf file and the database snpEff is using.

I have been using the hg38 database, and get this warning in almost 25% of my variants. This surprises me as I am using data direct from 1000 genomes and the latest hg38 database and was hoping someone may shed some light on why this is.

N.b. This is more a matter of interest than anything else, as I have downloaded the gencode annotated vcf files that 1000genomes website provide and can use them instead.

[GenoMax]

Check to make sure that chromosome names match in your VCF files and the genome you are using.