finding synonymous SNP'S

Question

[always_learning]

Hi all, I have an VEP annotated VCf file and want to know about all non synonymous SNP's. What will be the approach for that?

[Emily]

What do you want to know about them?

[always_learning]

I want to know about all NON synonymous SNP's from my VEP annotated VCF file.

[Emily]

Yes, what do you want to know about the non-synonymous SNPs?

[always_learning]

A list of all NON synonymous SNP's from annotated VCF.

[Emily]

Just filter your output file.

--filter "Consequence matches missense"

[GR]

try SnpEff.

Answer 1

[GR]

try SnpEff

Here are some usage examples if you want to do something similar