Q:
We are trying to implement the scores of Funseq2 (running locally).
However, we would like to have a score for each variation in the
input-vcf: this is not the case if we look at the Output.vcf.
Can I conclude from this output, that the missing variants in
Output.vcf have a score of zero?

A:
The somatic variants that overlap 1000 Genomes variants are filtered out.
Those might be the variants being removed from your output vcf.
You can check one or two manually and you should be able to confirm that.