This one is quite complex to explain, so i will start with an example
This is in my header
CADD,Number=1
CADD_SCALED,Number=A

When I have a multiallelic variant let say:
1 208063100 rs5780411 G GA,T

I would expect that CADD_SCALED has two values and CADD only one value.
This is correct when my file with the CADD/CADD_SCALED scores only contains this position once, when (in case of the cadd scores you will get scores for each ALT allele) you have multiple lines containing the same position but different ALT alleles it is going all wrong.
although CADD,Number=1, the CADD info field has now 2 values (for each ALT allele), and the scores has been flipped, the CADD score for ALT allele 1 has now the value of ALT allele 2 and vice versa

I included: input(input.vcf), output(annotated.vcf), conf(conf.toml) and annotationsfile (whole.vcf.gz + index)
vcfAnno.tar.gz