Tool:Snpeff - Annotating And Predicting The Effects Of Single Nucleotide Polymorphisms

Question

[Malachi Griffith]

snpEFF : A program for annotating and predicting the effects of single nucleotide polymorphisms

A variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

Typical usage:

Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).

Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here.

[bioinfo]

Is there any web interface where I can upload my vcf file and the reference genome and in return I will get the output?

Answer 1

[Richard]

I was looking for a tool to give me useful and easy coding annotations of indels from a VCF file.
So far this does everything I needed very quickly. Definitely worth checking out.