SIFT,PhD-SNP, ensembl, Polyphen-2

How do you use ensemble for SNP analysis?

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