Please, find out where the original VCF is and filter it using a proper piece of software (bcftools most likely). You simply cannot perform a reliable piece of analysis when you use excel to process a vcf - there are so many things that can go wrong and screw up all of your downstream analysis. Also, no offence to your supervisor, but it sounds like they shouldn't be in charge of a project with that kind of attitude towards data curation and software.

I would say there isn't much point at all in preceding with whatever analysis you are planning on doing unless you use a proper piece of software.

I also recommend seeing how you filter and transform the data correctly, and as mentioned above, the bcftools especially the query and view are very powerful commands https://samtools.github.io/bcftools/bcftools.html. Otherwise, you'll need maybe some more complex script in other languages: Python (pybedtools, pyranges,..), bash (sed, awk), R (vcfR), ...