Question: SnpEff, Exome Sequencing, Variant Annotation
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gravatar for avinashdhar123
2.5 years ago by
avinashdhar1230 wrote:

I want to annotate my vcf file against COSMIC database using SnpEff. How can we configure SnpEff to annotate a dataset using a custom database.

sequencing snp next-gen • 1.2k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by avinashdhar1230
0
gravatar for lakhujanivijay
2.5 years ago by
lakhujanivijay4.7k
India
lakhujanivijay4.7k wrote:

You can use SnpSift. If you can make a custom vcf, you can use that to annotate the SNP's

EDIT: Check out this as well

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by lakhujanivijay4.7k
0
gravatar for avinashdhar123
2.5 years ago by
avinashdhar1230 wrote:

Thanks for your prompt reply. The problem is that I am new to this field and need some sort of documentation from where i can read the instructions and follow suite. Can you help me with the same ?

ADD COMMENTlink written 2.5 years ago by avinashdhar1230

Ideally, start with reading Snpsift documentation itself as I mentioned above. Go step by step, like the first step would be looking for how to create the required vcf and from where. "Google" is your best friend. I am sure somebody has already did that.

Post specific questions on Biostars.

ADD REPLYlink written 2.5 years ago by lakhujanivijay4.7k
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