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SnpEff, Exome Sequencing, Variant Annotation

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.

next-gen sequencing snp
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written by avinashdhar123 • avinashdhar123

2 answers

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

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written by lakhujanivijay lakhujanivijay

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 ?

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written by avinashdhar123 • avinashdhar123

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.

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written by lakhujanivijay lakhujanivijay

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