Question: finding synonymous SNP'S
0
gravatar for always_learning
5.5 years ago by
always_learning1.0k
Doha, Qatar
always_learning1.0k 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 • 1.1k views
ADD COMMENTlink modified 5.5 years ago by RT340 • written 5.5 years ago by always_learning1.0k

What do you want to know about them?

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Emily_Ensembl20k

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

ADD REPLYlink written 5.5 years ago by always_learning1.0k

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

ADD REPLYlink written 5.5 years ago by Emily_Ensembl20k

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

ADD REPLYlink written 5.5 years ago by always_learning1.0k

Just filter your output file.

--filter "Consequence matches missense" 

ADD REPLYlink written 5.5 years ago by Emily_Ensembl20k

try SnpEff.

ADD REPLYlink modified 4 months ago by RamRS25k • written 5.5 years ago by RT340
0
gravatar for RT
5.5 years ago by
RT340
European Union
RT340 wrote:

try SnpEff

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

ADD COMMENTlink modified 4 months ago by RamRS25k • written 5.5 years ago by RT340
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