Question: finding synonymous SNP'S
0
gravatar for always_learning
6.4 years ago by
always_learning1.1k
Doha, Qatar
always_learning1.1k wrote:

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?

snp vep • 1.3k views
ADD COMMENTlink modified 6.4 years ago by RT350 • written 6.4 years ago by always_learning1.1k

What do you want to know about them?

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Emily_Ensembl21k

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

ADD REPLYlink written 6.4 years ago by always_learning1.1k

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

ADD REPLYlink written 6.4 years ago by Emily_Ensembl21k

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

ADD REPLYlink written 6.4 years ago by always_learning1.1k

Just filter your output file.

--filter "Consequence matches missense" 

ADD REPLYlink written 6.4 years ago by Emily_Ensembl21k

try SnpEff.

ADD REPLYlink modified 15 months ago by _r_am32k • written 6.4 years ago by RT350
0
gravatar for RT
6.4 years ago by
RT350
European Union
RT350 wrote:

try SnpEff

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

ADD COMMENTlink modified 15 months ago by _r_am32k • written 6.4 years ago by RT350
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