Unique mutations between VCF files

Question

[kshaffman]

I have two VCF files that are using hg38 as the reference genome. I am trying to find unique mutations between the two vcf files. What program should I use for this? I tried using vcfunique from vcflib, but was having serious installation issues. It does not work on windows, so I tried using a virtual linux machine, but I can't get it to work.

[LauferVA]

Do you have a prefered environment (R, python, etc.)? You could even do this with a one line command in awk or bash, but to do that you'd have to know a bit more about your VCF files (e.g. are they single sample or multisample VCFs).

[kshaffman]

Hi, the VCF files I am working with are each single sample files. My preferred environment is python, it is the only language I know anything about, but I'd be willing to use a different language.