Till now I've used SIFT, PROVEAN, POLYPHEN-2. What other servers are out their that analysis the deleterious effects of SNPs and their impact?
You can try "PredictSNP" which is very user-friendly. In fact, PedictSNP is a package of almost 9 SNP analysing tools
For Ensembl VEP, you can use the Web interface and follow the instructions:
http://asia.ensembl.org/Tools/VEP
VEP uses most of the available databases, so would be the free tool of choice.
You can also download the VEP apps (Unix) and run it from command line => require knowledge of Unix commands and VEP dependencies.
http://asia.ensembl.org/info/docs/tools/vep/index.html
If you are working for academia or research Institution (free licence), try ANNOVAR (again Unix based)
However, it is always best to write your own script and run against databases of interest.
I suggest the following web tools:
-https://cadd.gs.washington.edu/
-https://loschmidt.chemi.muni.cz/predictsnp/
-https://genome.ucsc.edu/cgi-bin/hgVai
-https://snps.biofold.org/phd-snp/phd-snp.html
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